So it sounds like you want to add some thought, memorability and danger into the travel time, but you don't want them to meta-game things so that they are overpowered by the time they reach their destination. You don't want them 'hanging around' these locales longer than necessary, over-foresting the fiendish-squirrels to extinction for XP. I would handle this a couple of ways:
Low treasure for random encounters
If you award XP by the book, with no extra 'story point awards' and keep treasure low to Nil (sorry the Dire Lions did not drop 100gp and a pair of bracers +4), I don't think they'll stay there long or advance too quickly.
Keep the CR level of the encounters in the Yellow Zone
I would keep it maybe at or a tick or two 2 above the party level; whether from sheer numbers of opponents (a large # of giant ant warriors) or quality (1 hill giant) or circumstance (see weather below). I think that most wilderness encounters are things that players should at least think about avoiding or fleeing from. These are encounters that should bloody them if they take them head on.
Roll encounters 'randomly' in advance
Roll a few (2 or 3) wilderness encounters in advance and write the results down on notecards so you at least have some idea of what they are going to be ahead of time. Helps to think about 'if this goes down, here's how it will go down'. Then for the encounter check, you are rolling to see if the encounter occurs (not IF it occurs and WHAT it is; you already know what the WHAT will be. You can also determine the encounter distance in advance or things like that)
Roll the Weather in advance
If there is going to be a lot of overland travel time expected, actually roll the weather up for the next three months. This (can) add a lot of flavor to encounters that do happen. Fighting a Troll in the middle of rainy deluge (or even a dry spell where the whole forest is ready to go up like a matchbox) can be a whole different ballgame from what players are used to. A swarm of Gibberlings in dense fog banks could also be unnerving; it is the Wilderness, so play up the different conditions that can happen there.
Track player supplies, and make foraging a dangerous challenge
In many of the classic fantasy novels, starving or dying of thirst is a real problem. This gets overlooked too often I think, or just 'handled' by someone making a Survival check at +10 or the like. Set some higher DC levels for different areas for foraging. When foraging, check for random encounters. (you might not be the only predator tracking that wild boar...) If an area has a low forage yield, it may be inhospitable, or there may be a real 'top of the line' predator around causing the imbalance.
Use Stalking encounters
Quite a few monsters (natural and unnatural) tend to stalk their prey for quite some time and 'wear them down' preventing them from resting, picking off stragglers. Wolf packs, Meenlocks and many others might come to mind here. Being in the wilderness means there is no safety. You may know 'something' is out there, you might even skirmish it into a quick retreat, but that doesn't mean it isn't going to come back a little later. Stalking is probably waaay underutilized in the wilderness.
Make it a challenge for the characters to exist in the Wild, and they'll not only remember it, they may feel relieved to get to where they are going.
I wanted to all an alternative from all the other types of posts I see (which more or less assume this is possible). That being said this is more my interpretation of how the rules are supposed to be viewed.
The rules for how you gain new spells as a wizard are fairly clear - you gain them as you level, based on your spell book. Now that being said, it is my assumption that a Wizard is already using his downtime to learn new spells, update his notes, and in general improve his spells. My example to support this is that a fighter doesn't just go to town, sit down and drink/sleep all night (well fair point, some probably do). But most are probably training, practicing their weapon skills, or improving themselves.
I would say the rules for Wizards also support this...
The spells the you add to your spell book as you gain levels reflect the arcane research you conduct on your own
Since if you are not doing this research in your down time, when are you doing it?
Aside: Now, it would be a separate issue if say the Wizard found a spell book, or notes about some spells he did not already know. But this strikes me as more of the role-playing side, and I don't intend to cover that in my answer.
If you decide to allow it, I would highly recommend making it massively less useful for your Wizard. A good method would be to use the spell copying table mentioned in other answers and use that as the time required (I expect this would dissuade him from trying anything other then the lowest level spells). It seems the rules outlined for this (both time and money) are fairly penalizing - I might also add a failure chance for a bit of home-brew flavor as well (e.g. the Wizard was attempting to write a spell he did not already know and did not gain through practical use).
Best Answer
I have had similar instances in the past involving required time-skip, or what I call "interrupted adventuring" for one reason or another. There is a few things I would recommend doing. First and foremost, just inform them of the situation from your side. Something along the lines of..
People are usually fairly happy with that on its own. However if they ask for something more here are a couple of suggested methods for dealing with it.