I'm going to suggest that not every monster needs to be wholly unique, and that your players will (probably unconsciously) thank you for reigning it in slightly.
This answer is based, in part, on an Angry GM article on traps, and partly on personal experience. In this case, they mesh well.
Players like feeling smart. They like to think that they've seen through the GM's (or the published adventure's) clever attempts to trick them. The cleverest trick is to let them.
Stable of Gimmicks
To that end, I would suggest first coming up with a small set of gimmicks that can be bolted on to existing creatures without affecting their CR too much (here's a place where the party composition can have a huge effect on the apparent CR of a modified creature; play around with the exact mechancis until it feels right for the party).
6 is probably a good number of gimmicks: small enough to remember them all, and it's a convenient die size. Gimmicks might include "acidic" or "strong"; an advanced gimmick might be "glass cannon". Each gimmick should include one identifiable trait and one mechanical effect (or two).
Sample gimmicks:
- Acidic: green tinge, can deal an extra 1d6 acid damage with natural attacks or has a ranged touch attack that deals HD xd6 acid.
- Fiery: orange tinge, aura of fire HD feet radius (round up to the nearest 5 feet), deals 1d6 fire damage, Fort halves
- Strong: looks particularly beefy for its monster type; +(1/4 HD, round up) strength
- Glass Canon: parts look beefy, parts look frail (eg., beefy arms, frail legs, or its weapon arm is out of proportion to the rest of it); +(HD) strength, halve max HP
- Agile: limbs look long and spindly; +5 feet to all move speeds, can ignore HD squares of difficult terrain per round
The particulars will depend on the effects you want mutations/magicks/... to have had on the local creatures. The important part is that they're easy to tack on and don't have a major effect on CR (which is why "Strong" adds to strength but nothing adds to constitution or even dexterity, since those will affect saves, HP, AC, etc.; strength "just" affects melee attack and damage, in a pretty straightforward way).
The gimmicks don't have to come from the same source on each creature (though, "Strong" probably will). One Acidic creature might spit acid while the next can throw it as an at-will spell-like (or supernatural) ability and the next is coated in acid (hence adding damage on a natural attack). One Fiery creature might actually be on fire while the next is simply supernaturally hot.
Choosing the gimmick could be done by die roll or by picking the one that feels right at the time (the latter is preferable if you're using the Environment, below).
And, don't worry if a gimmick makes sense for the creature in all cases; an Agile gelatinous cube or a Strong pixie are bound to show up eventually, if the mutations are more-or-less random (in-world).
Environment
Use the environment to help create unique encounters. Create interesting terrain features so that not all combats happen on a flat plane bounded by squiggles: chasms, cover, and cliffs can all play into making an encounter feel more unique, even if its the third "Fiery Centaur" encounter in a row.
You've said that this is post-apocalyptic. Has magic infused and mutated the landscape, too? Maybe Fiery creatures have fire resistance, so they tend to hang out around pockets of Fiery terrain (possibly magma bubbling up to the surface, possibly magical flames). Agile creatures will love ambushing creatures that wander into areas they've intentionally made difficult to pass.
Reward players paying attention
When players enter a new area, tell the players what (if any) gimmicks the area has. If the terrain is difficult, give a +2 Perception bump to the player who asks if those twigs might actually be an Agile creature's limbs. If the area is supernaturally warm, give a similarly minor boon (+2 to initiative, perhaps) to the player who breaks out the Frost dagger they found three levels ago.
If the players are in a dungeon (which is to say, a series of interconnected areas, which may or may not be underground), let them use this information to help choose which way to go. If they've got a scroll of Resist Fire handy, they might choose to go through the hot area instead of the frosty one. Giving players agency like this is a Good Thing(tm).
Not all monsters
Sometimes a bugbear is just a bugbear. Not all monsters need to have a gimmick. Especially if the players are new to the game, introducing a vanilla bugbear before introducing their Agile cousin will help them get a handle on the threats they're likely to face.
And, of course, sometimes a Fiery Kobold will just be friends with an Acidic one, and visiting in the "wrong" environment. Or, the Agile dire lion will be wandering through, looking for better hunting grounds.
Similarly, not all combat encounters need gimmick-ed areas.
Wrapping it up
Put together a small handful of gimmicks that you can slap on a creature quickly and that the players will learn to recognize so that they feel clever. Enhance with tacking the gimmicks onto terrain, so the players can make reasonably informed choices about how to handle unknown threats or make informed decisions about which path to take.
Make the encounter areas interesting and it'll feel like the apocalypse has had a greater effect on the world than a strict mechanical reading of the gimmicks might suggest.
