The biggest thing I've noticed a lot of games having problems with ever since I've been gaming is the fact that many games, particularly platformers and other 3rd-person games, often have very temperamental controls. It seems like control was first mastered with Super Mario Bros. way back when on the NES, and yet people still get this entirely basic principle.
This is very noticeable in the fact that many game reviews still comment on the tightness and quality of control in a game. I know Super Mario Galaxy controls wonderfully, but shouldn't that be expected? Perhaps someday it will be given that games control well, and we won't have to put up with this ridiculousness.
On a side note, I didn't even think of first-person shooters in regards to this topic. I play PC games most of the time, and FPSs handle just fine 99% of the time. (In fact, I believe that this is an area where good controls are generally not commented on, only bad controls are.) However, in my limited experience with console FPSs, many games just screw up the whole situation. Though not a big fan of the game itself, Halo really seems to have nailed the control scheme and succeeded where games before and even after have failed.