I'd like to see more extensive damage modeling. Not in every game - hit points are just right for UT and Quake - but plenty of FPS, RPG, tactics games could use it.
The bleed/bandage/kevlar/helmet/leg damage mechanics in ActionQuake, for instance, were way ahead of its time. I want that stuff back, in slower and more tactical shooters, and also in horror FPS like FEAR.
Another kind of damage model I want to see in some FPS is insta-death, but so that the player has powerful active defense measures (currently almost nonexistent in FPSs, if you don't count using movement to duck behind cover). I'm talking about things like an invincibility you can activate for a really short duration, a dodge/teleport to avoid the attack, deflecting a laser with a lightsaber, a really effective bulletproof shield, etc. These are essentially taking clues from the best beat'em ups, fighting games, shoot'em ups, and applying them in a FPS context.