I apologize in advance if this has been addressed already, but why is there so much contempt for these shooter game mechanics?
1) Auto-aim: Basically it adds a little extra precision to console FPSs, right? Because the all-superior mouse and keyboard aren't the standard control scheme for a console? So what's the problem? Sure, if it's magnetizing everyone's reticles into instant headshots, there's a problem, but the latest instance of it for me has been Halo: Reach and I'm not really any better at headshots because of it. Controllers lack precision in some ways. Also EVERYONE has it, so it's a level playing field. A wash.
2) Cover systems: It's a pretty logical type of mechanic, correct? We would take cover where we could, blind fire, all those things. I agree that if it turns every fight into a long-range game of whack-a-mole or you have an overly magnetic back it's bad, but a "cover system" isn't the problem, it's the way it's implemented. Obviously, this is more of a TPS mechanic, but I still see a lot of commentary on it.
3) Health regeneration: Also, shield regeneration. Ultimately, how a game balances the difficulty of making a kill is a choice of the designers. What matters is balance. Health regeneration is only a problem if it makes getting kills unreasonably hard when weighed against the other demands of the game. I like it. It means that finding cover can be a viable way to survive a fight and puts emphasis on efficient attacks. Especially good for a game with special weapons to grab. Then again, another game with quicker deaths and faster respawns can be fun too (TF2?). It's all about how it works for the game.
Feel free to add your own gripes about shooter game mechanics, defend those that come under fire, or ignore the entire post if this has been done to death.