Kai Leng from ME3: Already brought up, but I'll throw my voice into the choir of hate. The guy was a character so thin he could have turned invisible by turning 90 degrees to you, no cloaking device needed! "Oh, he's a biotic cyber ninja who totally kicks ass and wins all the time!". Shepard has more badass in her right foot than that guy has in his whole body. He's overpowered in cutscenes and only manages to do anything because the plot needs him to. His actual fight is meh (except for a few burns you fling his way, which made me smile. "I'm not the one who's always running" indeed!). It's a shame really, because I like the Illusive Man for the most part as an interesting (if sometimes odd) take on antagonists.
The Bloody Kid from ME3: Now, I know what some of you may be thinking. "The kid was a victim, how was he a villain?". I knew, the moment I laid eyes on him, that he was going to die horribly and it was going to be an overblown attempt at poignancy. And lo and behold, it was. The little dream sequences were to me more annoying than any of the fights, so I'll put him down as a psychological antagonist, even if he managed it posthumously. Then of course there's the Catalyst picking his form. And Shepard's supposed to feel bad about him? Shepard, who at this point may have sacrificed hundreds of thousands to save the galaxy, is supposed to feel bad about this? Sure, watching someone die up close is more harrowing, but she's a solider! With a LOT of experience! I don't see her having dreams of Jenkins or the Vermire Non-survivor. I dislike the clumsy way it was supposed to tug at my heartstrings. And it's really easy to get my empathy too.
Autum from Fallout 3: While I have plenty of loathing for him as a character (the death scene of James actually hit me pretty hard), I'm also annoyed by his bullshit survival and lack of closure. This is the guy who's made out as the final boss, but I'm fairly certain mooks are stronger than him by the time you fight him. Just some asshole in a coat and an unsatisfying fight. I don't mind non-combat villains, but they should have more satisfying endings than that. His death in the radiation he stupidly unleashed the first time would have been just fine, thanks.
Orsino from Dragon Age 2: Not necessarily a villain throughout most of the game, and actually an acceptable one if you take the Templar path at the end. But since I take the Mage path every time, his going over the edge in a fight we were winning easily just bugs me. You needed another boss fight? Send someone who actually makes sense. Cullen, perhaps, or even an early stage fight with Meredeth herself before she goes all One Winged Angel.
The Wise One from Golden Sun: Another "not actually a villain, really", but he gets a moment at the end of the Lost Age. Want to test people to ensure they're strong enough to have Alchemy released back into the world? Sensible. The method? What? All he's proved is that they're dangerous in combat and possibly sociopaths given who the final boss was. And more to the point, why would you pin the entire judgement of humanity's worthiness on that tiny group of very extraordinary (and thus non-indicitive) group of people? I love Golden Sun to pieces, and I'll admit a portion of my dislike of the Wise One stems from my enjoyment of Alex, but still, dumb move Wise One.
Seymour from Final Fantasy X: Not for the usual reasons though. What bugs me the most is that his plan makes zero sense even from his brain-dead position of "death=peace, so let's kill everyone". When people die in Final Fantasy X, one of three things happens. One, they are sent to the Farplane. This is the only way Seymour's idea could have made the tiniest bit of sense. But nobody lives to do the sending, so that's out for the most part. Two, people's souls become fiends. Who will likely fight, die, and then be remade into different fiends, perpetuating the cycle of violence and making his "peace" even more violent than Spira's current existence. Three, people become Unsent, but Sin or all the fiends will eventually kill them so it's back to the other two (by which I mean, actually only one) option.