It has been said, but Oblivion's scaling system is idiotic, because why on earth should I level up if it makes my enemies stronger? Isn't the whole point of leveling supposed to make you able to take on harder enemies?
Also, a lot of earlier RPGs simply fall under unplayable, when you put the game down for a week, and return to it only to find out that you forgot what you were supposed to do next. At least Fallout 1 and 2 had the Pipboy to help, so why don't Xenogears and the Final Fantasy games do.
Also, any game that has cover mechanics that makes chest high walls player magnets. Can get really frustrating really quickly.
The mag-charger from Time Splitters. For those of you not in the know, you could shoot through walls with it and see through walls with it. It doesn't do much damage, but it could still screw people like nobody's buisness.
Quick time events usually fall under this, at least if they are manditory.
Also, Dark Cloud had this game mechanic, where your weapon could break. Not a problem so long as you repair it, but then you find out that when it does break, it dissolves into nothingness. Dark Cloud 2 fixed that.
Also, any RPG with tons of characters and a non-shared XP pool. Yes, I believe you people were dedicated when you gave me 35 characters, but why bother when they simply need to be re-leveled. Final Fantasy Tactics was especially annoying with this. I did not go on a massive side quest just so that Cloud joins my party at level 1 (not that it matters, since he also sucks in other regards).
While on the subject of FFT, it broke the game halfway through the story with Cid, who was a one man army that does massive damage at no cost.
Resident evil had that funny mechanic that prevented you from aiming and walking. I would at least like to inch slowly backwards while the Spanish zombies came at me.
TESII:DF. Not their fault though, given executive meddeling was used to release the game sooner.