The inability to define my own controls. Presets are limited at times and usually are somewhat illogical or uncomfortable for me, and some games don't even offer presets!
Lack of thought or a design flaw. Sometimes it just seems like the developers don't play their own game. You see a problem and know the fix to it, and wonder how they didn't. Like for Fable 2's spell system, you can't really change the spells easily. A "spell interface" menu would have been nice, allowing you to quickly change spells in combat without having to navigate through a menu to do it. Gears of War and their "cover" button matched with the run button, so sometimes you'd cover when you just want to run by. To fix this they "made cover less sticky" when in reality it could have been "let go" next to go to cover or "let go and tap" or "let go and double tap". So, now the accidental cover problem still exists, it just happens less.
Mystery data. There are a lot of subtle things in games that the game itself doesn't tell you. The only way to find these things is usually from trial and error, or acquiring it from somebody who already did that. Knowing those things can sometimes improve your playing experience tremendously, and you can't help but wonder why you weren't informed of this by the game.
Inability to test play spells or abilities. Fable sort of remedied this problem with a "preview" but I find that the preview isn't enough, because I can't -feel- the ability, I can only see it. This problem is even worse with online games where the only way to reverse the selection in most cases is by completely remaking your character. Ouch! Better do a lot of research first, otherwise you might be in for a 20 hour marathon to regain lost progress because you simply HATE your selection to bits and pieces. Maplestory to those who have played this may be able to relate with job selections.
I probably have too many pet peeves to list, but I don't play a lot of games like I used to, so I only see a limited amount of them now. Very cool I must say!
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Permanently inane.