Here are a few things to consider :
Tactics
If a full attack is "all" it takes to down someone, force Move actions. Could come from cover/concealment or combat maneuvers like Trip/Knockdown or Disarm. If you just play "rocket tag", you're implicitly accepting that if you miss, there's a good chance you're dead.
Note that this is exactly what happens IRL between powerful forces in a battle and in this respect, is not a "bug" of the system but a simple truth.
Intelligence
So you're targeted by a Master Ninja, who manages to sneak up on you and place a Death attack. Curse you, Hayabusa ! Wait, you made your save ! Time to grab your trusty bow and fill him with arrows...
Well, boo. The ninja has broken/stolen your bow as well. Not only does he make his escape, he's slowed you down by forcing you to have it repaired / replaced while you try to get it back.
This goes a step further in Tactics, and is to be expected of Ninja, for example. Study your target. Know their strengths and weaknesses as well as yours. "That Brilliant Bow of Badassitude could be a problem if I must escape. Can I get rid of it ? What about impairing the bowman ? Maybe I could blind him ?"
As an aside, the GM should make sure the players don't feel cheated though. Extreme competence is assumed as part of the characters (especially past level 10) and robbing them of that can be frustrating to no end for some.
Numbers
So they can take the Big-Ass-Monster down in a round ? What about 10 Medium-Sized-Nuisances ? One by itself could barely hope to hit them, but with flanking, teamwork feats and simply being all over the place, the little pests could prove to be annoying. Add in a Leader-type and you could even be worrying your characters.
Story happens
Take the characters down a notch or two through Story. Have them stripped of Rank and Privileges by the King or even make them straight Outlaws. Have them stranded on an island (and some of their equipment lost to the sea) after their boat got caught in a storm. Have their home base attacked (and their Mentor killed, leaving them unable to progress in their main class) while they were on mission.
Change focus for a while
Once all is said and done, if the combat has become so easy it's boring, it may be time to try a little courtly intrigue for a change. Or why not a mystery ? Possibly meshing with "Story happens" above, there are plenty of opportunities to take the players / characters out of their comfort zone while staying true to the setting. They'll be happy to resume bashing heads once they've stumbled for hours finding a tangible threat to pounce on. Or hey, maybe they'll actually enjoy trading piques with the Jester and decide they want a piece of land and a throne of their own ?
Unfortunately, blood biography combined with magical checkins and a spell-based binary search (probably using spirit planchets and generations of "retired" agents as spirits) to locate bodies spells doom rather cheaply as government spending goes.
Blood bio, cast with a drop of a ctreature's blood, gives answers to:
Who are you? (The name by which the creature is most commonly known)
What are you? (Gender, race, profession/role)
How was your blood shed? (Brief outline of the events that caused its wound, to the best of the victim's knowledge)
When was your blood shed?
Finding the corpse will have blood in its wounds, which then provides a "brief outline of events." It is reasonable to assume that a brief outline will discuss the method of attackers. Which then, (papers please!) will link them to the last internal checkpoint by their class descriptions or other characteristics linked to their identities.
To be clear though, the public side of things will be absolute silence. Because the public doesn't know about this appearance of weakness, there will be no advertising the weakness. (Otherwise people get the idea that harming the secret police is possible, and we just don't want that...) Reprisals are fine and all, but an aura of omnipotence is better. If the team missed any of its checkins or procedures, their supervisor (to the function of his ability to have fall-guys) will be tortured to encourage the others. If there are some rumors, some of the "usual suspects" will be rounded up and executed for a trumped up charge.
In terms of team notification, every team will, being lawful, likely follow "modernish" police practice of "check in with home base." The logistics of this vary, depending on infrastructure.
- Visible tech: A napoleonic semaphore is not out of the question, especially with items of "whispering wind." (Given how cheap this makes individual messages, combined with the efficiency gains from modern communications and the ability to spy on the communications of a populace, I see no reason why a lawful evil society wouldn't have one of these networks.)
- A wizard did it: Telepathic Bond may be made permanent. Every squad of agents should be placed in telepathic bond with their controller "back at base". Given the communications capabilities that this implies, it's the cheapest possible communications network. An "empire" (evil or not) lives and falls on its communications, which means that there should be a correspondingly high priority assigned to this. We can assert, however, that the idea of battle-ready flying squads ready to teleport to help requests may not be part of the repertoire, likely due to infighting and other politics. Still, even presuming that these aren't "always on" (maybe the controller is managing multiple squads) squads should check in when before they expect trouble and after they're clear.
The players get one missed checkin as a grace period, Then a "ministry of divination" (I'm assuming nation-state resources) steps in with a series of spirit planchettes and does a binary search to find the last location of the missing team (as a function of the region that they checked in from). The binary search only needs to be of a region the size that locate object (remember, both a corpse, the corpse's robes, and the identity documents marked with a specific arcane mark are all items) can cover. Happily, the players removed some of the evidence there, but a corpse is still an object.
That binary search takes exactly as long as you wish, as it's a function of the resources invested into the "ministry of divination"'s binary search capabilities and whether or not the "spirits in the area" are favourable to which side. Of course, if I was an lawful evil ministry of divination, I'd make sure that the spirits in the area were particularly well disposed to me: any spiirt that provides a useful answer has their family rewarded with a lowering of quota or other "random" bureaucratic positive outcome. Any spirit that obstructs this will a) have their family harmed, and b) be otherwise removed using normal mid-level adventurer capabilities.
If I was doing this in 3.5, I'd make sure that the communications infrasturcture all had the necrotic cysts implanted in them so that the parent-cyst could scry (and remote take over) any of her agents whenever she desired.
Best Answer
There is a mechanic that you could adapt from Blades in the Dark (at least, I think it was Blades in the Dark, it's been a while). Basically, instead of asking everybody to run Athletics and be done with it, you tell them that they need to achieve a given amount successes in order to escape. The way they achieve them is totally up to the players, but they can't just mindlessly repeat the same action, they need to try different things each time.
For instance, you could tell a group running away from a monster that the monster is really on their heels and they need four successes to escape. You can even draw four squares on a bit of paper and check one off every time they achieve a success.
Probably they are going to start by trying to outrun the monster, they might roll athletics and succeed, then you check one square off and say "alright, you've put some distance between you and the monster, but it's still running after you, what do you want to try now?" Now they might try to hide from the monster, set it on a false trail, or disguise themselves to scary it off. The more things they try, the more crazy ideas they are going to come up with, and you can always ask them to narrate each action if you want some more juice (if they say that they try to appear scary to scare off the monster, ask them to describe how they are doing it, not only roll dice).
This mechanic can, of course, be used for any other kind of challenges, not only running away from scary creatures.
To make it more interesting, a critical success can count for two and a critical failure can set the party one success back.
Active opposition
There are at least three ways you can go if you want to add active opposition to this mechanic.
Add a challenge for the opposition. The opposition needs to achieve a given amount of successes, like the party. It can be the same or a different amount, but keep track of it separately from the party's. Whoever achieves all the required successes first, wins the challenge. This works better if both sides are trying to achieve the same goal, like a race or an athletic competition.
Make the opposition set the players back. The opposition might do some actions that, if they succeed, add one more success to the amount required by the players. For instance, in the running away example, the monster might trigger an avalanche to cut the player's escape route. Then you would draw one more square in the paper with the amount of successes required for the challenge.
Add a time limit. If the party don't overcome them in a given amount of rounds, the opposition wins. The opposition is not really actively preventing the party, but the end result is not too different.
If I recall correctly, the first one is in the rules for Blades in the Dark, but the second one isn't, because the system puts a strong focus on the players driving the action. If you want to use the second option, I recommend to do so sparsely, and in any case I wouldn't make the opposition make actions that may set back the players more than once or twice for challenges that are not already difficult.