So you only have enough time for either finishing off the adventure, or dealing with random encounters, but not both. Therefore any solution requires spending very little time.
Simple Narration
One acceptable way to handle it seems to be to narrate it away. It's entirely legitimate to narrate their travel through the wilderness and cut to the chase, so to speak. Your players won't object, and are even likely to be thankful that you responsibly paced the session so that it had a natural and enjoyable end.
I wouldn't bother with any resolution mechanic, even a simplified one. Sometimes travel in the wilderness is uneventful. Take advantage of that, plus your power as the controller of the world and your responsibility to pace the game well, to just make this time one of those uneventful travels.
If you feel that it is really unrealistic for this trip to be uneventful, mention what trouble they encounter along the way in the past tense, off-handedly, and conveying that "of course" they handled it without any difficulty. For example, encountering and quickly dispatching an already-weakened patrol of orcs can be glossed over in a sentence, giving them your acknowledgement that the PCs are kick-ass and that was nothing to deal with. Lead right into a description that places them about to engage in the final action of the session and you're good. In systems where encounters lead to XP of some kind, I wouldn't hesitate to give them a token amount – unless the resistance was really beneath them.
Alternatively…
Roll For Complications
You don't want to take any time dealing with the travel, but that doesn't mean it has to be meaningless. Taking a page out of Dungeon World, you can call for a roll to test something during the "perilous journey". Decide on a possible complication of the journey that might lead to a mild consequence for them to deal with at their destination.
Perhaps you have them check if they move stealthily, and when they arrive the inhabitants have been warned of the approach of armed people, or not. Perhaps they make a survival check to determine whether they arrive hungry. Perhaps their pack animals were spooked at some point, and an animal handling roll will determine whether they're down one donkey and low on torches and lamp oil as a result.
Whatever complication you think will be interesting, present the potential event, describe the possible consequence, and call for a single test of their abilities to do well. If you like, you can come up with two or three (quickly), and give the players a choice about which one they want to risk on a die roll (they get success on the others free). This is a very quick and flavourful way of making the travel meaningful while concentrating their attention on the important thing: the final action of the adventure.
Travel Is Awesome!
Focus on the journey, not the destination. Joy is found not in finishing an activity but in doing it. ~Don Williams, Jr.
Far from being something to "skip over," wilderness travel is an interesting part of a story and forms a large part of many narratives, from Lord of the Rings to Star Trek.
From the 1e Wilderness Survival Guide to the more specialized 3e books like Stormwrack and Sandstorm, there is a lot of material to draw on in order to make wilderness travel more arduous and interesting.
For inspiration, I like reading historical travel narratives - ones that go through the jungles of Africa are especially juicy when it comes to ideas of how the landscape can terrorize the unwary traveler.
Weather
The rain falls upon the just/And also on the unjust fellas/But mostly it falls upon the just/Cause the unjust have the just's umbrellas ~Cormac McCarthy
It's simple, but get a random weather table and generate weather each day. (Obvious corollary - have seasons!) Climate has enough perils for most folks! In my current piracy-based Reavers on the Seas of Fate campaign, there's a lot of sea travel. Wind strength and direction can speed them on their way or stop them in their tracks; storms can provide vigorous skill challenges to a ship's crew! Getting wet, getting cold, getting overheated, getting fatigued all contribute to the wilderness travel feel, and give real bonuses and penalties the PCs can't ignore in combat. Have a combat in high wind or a rainstorm and apply the rules for it; it's quite a change of pace! And besides that, it is probably the single biggest addition to the sense of realism, to have variation going on independent of the PCs' actions and desires. Makes the world seem bigger than you are.
Survival
My time in the Boy Scouts taught me that Nature has but one goal - to kill you. ~Me
To get along in the wilderness, you need food, water, and gear. If you're not familiar with the land, you will end up having to backtrack around (or walk into if you're really dense) rivers, ravines, animal/monster lairs... More esoteric threats like quicksand also dot the landscape. Disease is always a threat as well. Insects plague people (and bring more disease) in many different terrains and seasons.
This is a great opportunity for those Survival and relevant skills to come into use. I prepare lists of "random encounters" that are more mundane than monster stuff and make them (and monster encounters) dependent on Survival checks. Skilled woodsmen don't walk into an owlbear's territory or drink too much from water in a cave.
Getting Lost
Not all those who wander are lost. ~J.R.R. Tolkien
You also need maps or guides - besides avoiding trouble spots, it's really quite difficult to find your way across trackless wilderness. Plenty of people get lost on reasonably well blazed hiking trails in the modern day, and having a map (and a compass, and other stuff) in no way guarantees you can't get lost. Time for Survival again!
In my pirate campaign, I require a whole lot of navigation rolls to find things, even when on a chart. It's very not simple. And when you get lost, you run into other stuff, you take more time to get there, you get more wear and tear...
Fatigue
Travel is glamorous only in retrospect. ~Paul Theroux
Wilderness travel is tiring and wearing, and not just to the people, but to gear as well. If they spend a lot of time out in the elements (and especially if they ignore rain, bogs, etc.) then their gear will degrade.
But mainly people get tired. Some of it is from the elements and disease, above (note that in 3e, a lot of the heat and cold stuff ends up imposing the fatigued condition). I'd consider giving nonlethal damage or even ability score damage from some of the natural threats from the "Survival" section above. "Stinging gnats - Survival DC 15 or 1 point of CHA damage."
Then, finding safe places to hole up and rest can provide mini-adventures of their own.
Inhabitants
Travelers never think that they are the foreigners. ~Mason Cooley
Depending on the region, someone or something lives there. If it's free of people, it's probably large herds of animals of various sorts that definitely provide obstacles and threats. But usually it's people. Many of these people don't like visitors and may attack, or demand tribute to pass. Or they do like them, and insist they come, eat, interact, get hit up for various stuff (and if rejected, get hostile). And you're a lot more likely to come across inhabitants than just as "wandering monsters" - the more-hospitable points of the terrain you'll want to travel through, camp in, get fresh water from, etc. will be hot spots for the locals too. And word spreads; if you slaughter/give syphilis to/give loads of money to any given village, the ones nearby will find out quick. Local culture is as much part of the landscape of a trip as the real terrain features, and should be memorable.
I fondly remember the Night Below game I ran where the PCs stayed the night with some friendly gnomes in their burrow. Their elder told them a chilling story about the legendary dark elves, and mentioned that their caverns once extended to below this very burrow... When a dark form broke through the dirt wall of their room that night, the wizard freaked out and Color Sprayed the party fighter into a coma. Of course it was just a puppet on the end of a broomstick being pushed through by giggling gnomes in the next room. I'm pretty sure that the players as well as the characters still have the emotional scars from that session.
Roleplaying
I have found out that there ain't no surer way to find out whether you like people or hate them than to travel with them. ~Mark Twain
I still remember the 2e game where the PCs holed up in a rural inn for two days waiting for a big rainstorm to let up; as the stir craziness set in they got up to shenanigans more interesting and memorable than the adventure at hand. Not quite the Donner Party, but getting there.
Travel is often an opportunity to slow the pace and have PCs interact with each other (assuming you're one of those weirdos that does such things instead of just slaying monsters). Once you hit cities it's intrigue central; once you hit the dungeon it's hardcore killing action. It's during the journey that you can get PCs to take the time to develop themselves by talking with others.
And it's just gold if there are regular NPCs with the party - this is the time for their personalities to develop, for drama and seduction and all that Real World/Survivor/Insert Your Favorite Reality Show Here kind of stuff.
Combat
Unless you know the mountains and forests, the defiles and impasses, and the lay of the marshes and swamps, you cannot maneuver with an armed force. unless you use local guides, you cannot get the advantage of the land. ~Sun Tzu
If a fight happens, don't let them forget where they are. In the wilderness, nice level stable footing is the exception not the rule. Maybe it's raining, maybe they're on a riverbank, maybe it's 8 PM and it's twilight, maybe they're in a marsh, maybe there's hanging vines everywhere. Once it goes all combat encounter, you should under no circumstances have everything morph into a featureless battlemat. If you do not weave the description of the surroundings into your GM descriptions at least once per round, you're not doing it right.
And keep in mind the locals know the terrain and will use it to their advantage whenever possible when engaging the PCs!
Best Answer
I see two primary ways to approach this, depending on the travel. (TL;DR at the end)
Travelling through civilized lands
From your description, it seems like your players (who are, considering you are playing D&D4e, are basically powerful heroes) are travelling between two cities in a civilized nation. In this case, I'm not even sure if I'd run any kind of straight forward combat encounter. After all; it's not much of a civilized country if random merchants have a high chance of bumping into something that's a threat even to a group of adventurers. They would be scared to travel that road, and with good reason.
Instead; make a list of random encounters that highlight the kind of things you would expect to see on such a road. These can be short (like a few minutes), focused on roleplaying, and highlight exactly the things that make this part of the world unique. They can be dangerous situations, but they should be dangerous for others and mostly resolved by talk. They can also simply be amusing, peculiar, atmosphere building, or setting up for later adventure.
Each should have one or more actors and a situation that is happening. (Those without actors other than the players are usually boring; those with actors but no situation are usually just ignored)
I don't know the setting you're using, but I'll try to make a list of the kinds of things you can run:
Generic Actor examples:
Next, come up with a suitable situation for them to be in. Maybe two of these groups have bumped into each other. Perhaps the nobles ran over one of the farmers, and now he's wounded. Maybe the military patrol is questioning and intimidating the lone merchant. Maybe a travelling cleric is annoying a hunting party. Maybe the bandits are ambushing someone just as the players approach.
Let them roleplay through a few of these simple situations, interspersed with "for a few days, nothing interesting happens.". This will give them an idea that things happen in your world; you get some chances to tell of the changing terrain (seeing more and more military patrols in these little encounters would reinforce the idea of heading into a dangerous or militant country, while meeting more travelling bards would give a very different kind of country)
(If you run something along the lines of "you find bandits ambushing a farmer", don't grab the dice. Run it more like either the players scaring off the bandits and the farmer thanking them, or a hostage situation. These bandits are no match for the players and they know it)
In addition; if you want to highlight the strain of long time travel with a bunch of quirky people (like most adventurers are), ask each of them beforehand to give you one description of something his character does during the trip (or does in general) and then for every long travel randomly pick one of these things and use them as a highlight in the travel.
If your party Elf has told you that he likes to sing during the journey, run one short encounter that starts with "Today has been calm. For the 10th day in a row, the Elf has spent most of the past 6 hours singing.", followed by a bit of silence. If the players care about interparty social interaction, they'll probably jump on that cue and have a few interactions. (If they don't care, they won't but you probably can't make them anyway)
The more of these short moments you have, the longer the trip feels. If the players are preparing for a long trip then you shouldn't feel bad spending an hour (or two) just doing a bunch of these. I've spent half of my last session mostly like this; just the players bumping into various characters from the region they were in.
If your players start getting bored, you can consider throwing in something with a little more threat but an easy option out, so the players can decide whether they want to pursue or not. Instead of having a Hydra come crashing onto the path, have someone bump into them and warn them that he's seen a Hydra in a nearby cave and that he's scared it'll attack a nearby village. It shows them the world can be dangerous, without being continuously attacked by things, and gives them the option to roleplay saying "no".
Travelling as an adventure
When a travel is through more of a wilderness area and for long duration, you should treat the voyage like an adventure in itself. Map out some things that are going to happen on the road (these don't even have to be random) and then see what the players do.
Make sure you spend some time at the start where the players prepare for their journey. Let them get some information about likely things to encounter (in terms of terrain, weather, villages, monsters, dungeons, etc) and give them time to prepare for these things. As they start on their journey, use short roleplaying encounters as described above as they set off, but alternate them more and more with encounters with more dangerous and uncivilized opponents. Their journey does not start in the wilderness most likely; so as they set out they will meet some merchants and workers, then at some point mostly military partols and some workes, then military patrols and the occasional savages/monsters, then at some point only wilderness encounters.
All of the wilderness encounters should still have a situation that doesn't immediately involve combat. Running into a party of Goblins that try to kill the players is a cliché, but running into a party of Goblins that are picking berries can also be very interesting (and quickly turn into the former if the players approach it wrong!)
When it comes to the players maybe facing something much more powerful, that's also a case of foreshadowing. The odds of two entities traveling a land to randomly run into each other is very small. However, if one of these two entities is trying to find the other, the chance goes up considerably. But that also means you might get early warnings. This is then the best way to set up the atmosphere for a "random" encounter.
Consider the following series of encounters:
The above is, ultimately, the same as just pitting the player against a Dragon in a featureless plane, except that now the atmosphere is set, the players get ample opportunity to come up with plans to avoid this Dragon, it doesn't feel random, the players will probably not go "oh a clearing, time for some random encounter" (even if they know exactly what is going to happen) and it'll feel like they've been travelling for quite a while.
Likewise, you can use weather effects without dice rolls if you make them a part of the story. Rather than saying "it rains, roll Endurance", you can simply make the observation "dark clouds gather overhead. you remember the warning the villagers gave you about how rain can keep coming for days on end." and go from there. If they decide to travel through it; tell them how they get chilled to the bone. Ask them how they'll deal with that. Only use dice when they keep ploughing on without taking any precautions. (And make those dice hurt)
Giving them foreshadowing, the option to adapt their plan, and letting them avoid much of the nastiness if they came prepared makes the world come alive. Having 3 short encounters where the rainfall is described as "continuous" makes it feel like the rain is really, really bad. Players will learn to measure travel by how many small things happen on the road, and anything that keeps happening during all of them will also start feeling really long.
Extended example from my last session
Setting
This took place as my players prepared to venture from their old city towards an ancient, abandoned temple to the dragon god of culture in the hopes of fixing their dead friend. They knew very little of the place other than that it was abandoned and lay deep inside Kobold territory.
Prep
At this point the players had the option of making their own plan. Main part of the plan was the party Druid going to have a chat with the Kobold Druid who was a member of his circle and responsible for the Kobold kingdom. This meant a roleplaying encounter where the Druid first talked with the Kobold ingame. They learned that they needed papers to travel safely.
After this, the players took some time to gather their stuff, bought some travel gear, and set off.
First encounter
Shortly after entering the Kobold lands, the players encountered the Kobolds; one of their Sorcerors and his bodyguard blocked the path and interrogated them. Remembering what the Druid told them, they asked for travel papers. After some haggling the Kobold sold and prepared their travel paper. He also explained the rules (no digging, no cave exploring, no entering Kobold settlement)
Second encounter
After shooting a deer, setting up camp and having dinner, the players go to rest. The following morning, the remains of the deer have all gone missing. The guards hadn't noticed a thing until it was gone, but scouting in the morning finds various tracks of Kobolds around their campsite.
Third encounter
Travelling further, the players come near a Kobold village. Again they run into bodyguards, who ask them about what they are doing near the village. After a show of papers the guards send them back around the village and they continue on their way.
Fourth encounter
In the woods ahead, the players come across the corpse of an Ogre. It seems to have been killed by small stabbing weapons. Doing some research around the site, the players learn that there's more Ogres that left the scene, but no sign of any struggle or marks of other creatures. A little worried, they push further.
Fifth encounter
From up ahead, the sound of giant feet can be heard. Ahead of the party, two Ogres burst from the path, in obvious panic. In an attempt to regain their composure and hide their fear, they act tough and threatening to the party, which takes no time to answer equally tough and a short fight breaks out. (The Ogres are not much of a challenge)
The players wonder amongst each other what scared these Ogres so much, and remembers the other corpse they found. More worried, they push on.
Sixth encounter
The morning after battling the Ogres, as the players break up camp, they encounter a necklace made from Ogre teeth hanging near their tents. No tracks of any creature can be found, and the night guard hadn't noticed a thing. The players decide to put up an extra watch from now on.
Seventh encounter
After a few days of finding little but the occasional Kobold guard near a village (at this point they've seen enough of them that it becomes mundane, and they are mostly just a quick reference unless they have something important to say) the players start coming closer to their goal. During the day, they notice a hawk that seems to follow them around. In the evening, as they make camp, the hawk sets down nearby to watch them. The party Fighter, being ever the pragmatist, decides to shoot it. The following morning as they wake up, the Ogre-tooth necklace has been stolen, although the Fighter was wearing it as they slept. The night guard, again, saw nothing. The players are now extremely worried, but realise they can only push further.
Eight encounter
The players spot an abandoned castle on a hilltop. Curious about whether this is their destination, they decide to ask the nearest Kobolds about it. The Kobolds tell them the place is haunted and they never go there, but it's not the temple they are looking for.
The word "haunted" seems to draw the party's attention, and they decide to check it out in hopes of finding treasure.
Ninth encounter
The players check out the castle, which indeed turns out haunted. As they walk around, various mysterious things happen (fires suddenly going on, wind blowing inside buildings, rumbling sounds). As the players are eager and continue to explore, I realise they are probably looking for something exciting, so I fill in the haunt by having Elementals appear from the castle, which engage them. The players realise they've bitten off a bit more than they can chew when after the first wave, a second, much larger Elemental starts to form nearby, and quickly leave. (I make a quick note that they might want to come back here later)
Tenth encounter
The players push further out, until they see in the distance two openings in the woods, fairly close together. At their next chance they again ask one of the Kobold guards whether this is their target. The Kobold explains that one of the two is a large Kobold city, which is off limits, and the other is their goal. He also tells them the Kobolds never go near the temple, or the city it's in, but that it's all on them what they do.
Arrival
The players arrive at their destination after a long, dangerous journey through Kobold lands. They are still full of questions about the Kobold empire and the strange things that happened to them, but they set it aside. As they travel inside the city, many more exciting things happen, but their travel is over. It took about 4 hours ingame time if I remember right, and certainly felt like an adventure. And of course, there´ll be a trip back if they make it through the temple. During that return trip, at the very least they´ll run into the mysterious Kobold Giant Hunters they heard all these rumors about...
Summing up
TL;DR: