Hmm...
Unit restrictions and bad resource systems: Choose between a) two guys with sharp sticks, or b) an economy - but not both, not ever both!
Training a single soldier at a time: I need to build four Barracks/equivalent to keep unit production above .5 soldiers per minute.
Walls in Fighting games: repeatedly tapping kick at someone who is unable to move isn't fun, stimulating or terribly realistic
Half-arsed Character developers: who can't be bothered with balancing characters, I'm looking at you Hworang and Eddy
Sniper rifles; Its a precision weapon that takes a shit load of training and practice to be able to roughly hit what your aiming at, not God's own hand...
Jumping puzzles that aren't affected by the difficulty setting: I have no problem with Prince of Splat's various enemies, sometimes their challenging. But jumping stupidly massive gaps over and over is not challenging, just annoying...
QTE: I think the majority of developers who make games with a QTE haven't actually played their own. I will concede some are rather good and make it very satisfying, but so many don't.
Grinding online: Isn't the point of online gameplay to socialize? Or at least make a human somewhere cry?
Like GTA but: Arrrggh!!! Free-Roaming needs something special to be worth playing, GTA has originality, it was the Prime, Destroy All Humans has mind-reading and an anal probe, Mercenaries had decent combat.
Vehicle Sections: See Like GTA but, but add Hollywood Car syndrome.
Durability: Its a fucking sword, its meant to cut things!!!
Stealth: Only if the entire game is meant to be about sneaking. Not if Johnny Shootsalot-McMinigun