I have to echo the "one button for multiple tasks" sentiment. How many times did I get killed in ME2/3 because Shepard decided that my command to take cover was a command to vault over the piece of cover, right into the line of fire?
One that's specific to Assassin's Creed 4 would be the way they handle optional objectives. I'll start a mission, be given my main objective but not the side ones, and then get caught up in the mission and not notice the popup telling me to kill 2 ships with one broadside shot, for example. Yeah, telling me the side objectives right at the start might spoil some stuff, but ffs don't force me to pause the game after every event flag just to see if I missed the gd popup.
Missable items in games like Fallout 3 and Skyrim. It's not as big a deal in, say, Bulletstorm, because that's a short game that I don't mind starting over if I miss a skill shot or whatever. In a game like Fallout 3, when I miss a bobblehead and have to either let it go or go through 30+ hours of gameplay again I die a little inside.
And finally, a non-videogame example: Wizards of the Coast's policy with regards to the Magic: the Gathering modern banlist. Deathrite Shaman is a TOTALLY FAIR CARD. Their reasoning for banning it was that it is efficient at all stages of the game; in other words, "this card's good so we must ban it!" I don't even play Deathrite, in fact the deck that suffers the most from the banning is my worst matchup so it's actually good for me personally. It just pisses me off that the solution to good cards being played a lot is to ban them rather than, oh I dunno, unbanning some of the OTHER good cards they've banned to give players other options. Seriously, people pay a lot of money for decks in this format because it's supposed to be non-rotating (ie. you can play your deck forever without worrying about the cards leaving the format). At least with rotating formats players know exactly how much longer their cards are going to be legal.