In Xenogears, Kahran Ramsus appears as a primary villain early on, and, with his prettyboy features, white hair, and usage of a sword as his weapon, seems destined to be the big bad. By the end of the game, his wallflower-like personal assistant has turned out to be the real Big Bad, he finds out that he's a failed clone designed to mimic the powers of the main character (who he has repeatedly lost to), and is abandoned by his masters for his repeated failures.
Vyers: I see. So you saw my potential and decided to strike first against moi... Such wonderful intuition... Well played, son of Krichevskoy. Laharl: I've never even heard of you. It's only a coincidence that we're here. You're just a tiny stepping stone on my path to the throne. Vyers: * gasp* How dare you! I'm the Dark Adonis Vy... Laharl: Who gives a damn about you? Your new name is "Mid-Boss". Mid-Boss: M-m-mid-Boss!?
Winston Payne from the Ace Attorney series, while not a villain, is a prosecutor, and therefore an antagonist. He was once the famous "Rookie Killer" who claims to have never lost a case in his first seven years as a lawyer, but lost one case along with his hair and, from then on, basically became a joke.
Dist from Tales of the Abyss certainly comes off as one, introducing himself as 'Dist the Rose' but ending up being called 'Dist the Runny'. In every fight, he sweeps in with an over-dramatic entrance and then gets made fun of immediately, usually by Jade, before his humiliating and undignified loss.
Pete from Kingdom Hearts II, and loads of it. Seems more like he just picked the wrong side.
Demyx arguably fits in the same category, especially in Days. All he wants to do is chill with his sitar, and Saix and Xemnas make him act evilly. Averted later when he puts up one hell of a fight.
Steambot Chronicles has Dudley, an obnoxious, tough-talking, muscle-brained trotmobile rider who the player runs into on about 4 occasions (3 during the main story and another in an optional encounter). While not necessarily a villain per se, the oaf constantly boasts about his strength and generally acts like a prick (he picks fights with anyone he can, destroys a farm just because "flowers are stupid", and think that a massive zeppelin is hoarding treasure). In the hero ending of the game, he can even be seen during the credits making what appears to be threatening gestures towards Vanilla (who is leaving on a ship for his homeland).
Halo has the Unggoy/Grunts, the main cannon fodder for the Covenant. Small (by Covenant standards), requiring gas masks to breathe in non-methane atmosphere, mistreated by the other races, they're slaves who come across as cowards. In large part because, fearing an uprising, the Covenant doesn't want to give them any actual combat training. Half the fandom feels sorry for them. The other half loves to slaughter them. Averted in Halo3 and Halo3: ODST: there, they take so many levels in badassery.
Professor Nakayama in the Borderlands 2 DLC add-on "Sir Hammerlock's Big Game Hunt". He's evil, sure, and has a plan that he simply can't be allowed to carry out, but he's also scared out of his mind by the player characters. He sees you killing his minions with ease and is frightened by your power — he's a bad guy but not a brave, confident, or competent one. You don't even get to fight him. After putting a stop to his "plan", he walks out to confront you himself... annnnnndd promptly falls down some stairs and dies. Thus, you're spared from feeling like a total prick; he's just that pitiful.
Given that he does try to kill you upon his first appearance, Zevran of Dragon Age: Origins counts as this for all of five minutes before he joins your party (or you finish him off, if you decide to be a bastard). Jowan is a slightly straighter example, owing to how many of his life plans blow up in his face.