Jr. Troopa from the first Paper Mario tries so hard to be intimidating and actually puts up a bit of a fight later on, only to be humiliated and beaten by Mario on a regular basis. The game also allows you to jump on him, hammer him, hit him with Kooper's Shell, and even bomb him. The poor guy even gets frozen after beating him in Shiver Snowfield. Yet he never gives up.
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 (even when compared to Puny Earthlings), requiring gas masks to breathe in non-methane atmosphere, and mistreated by the other races, they're slaves who come across as cowards. This is 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. That said, from Halo 3 onward they take several levels in badassery (even if they're still lovable cowards at heart).
Professor Nakayama in the Borderlands 2 DLC add-on "Sir Hammerlock's Big Game Hunt". He outright has to beg the Vault Hunters to come fight him, since they're more interested in hunting with Sir Hammerlock. Once the Vault Hunters decide to thwart his plans just to shut him up, he immediately realizes how deeply in over his head he is as the Vault Hunters mow down waves of his best minions and destroy crucial components of his plan with minimal effort. Sure, he's trying to clone Handsome Jack, and he's succeeded in creating a handful of genetic abominations, but a criminal mastermind he ain't. 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. He's even more pathetic in the Pre-Sequel, in which he is characterized for his obsessive crush on Handsome Jack, and his incompetence in the realm of science gets highlighted even further; apparently he had to lie about his doctorate to even get hired by Hyperion in the first place. Then again, in Tales from the Borderlands, it's revealed he managed to perfect his Jack AI sometime between the events of the Pre-Sequel and Sir Hammerlock's Big Game Hunt, causing a lot of problems for everyone.
Claptrap: Man, what a loser! And that means a lot coming from ME.
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.
Wheatley in Portal 2. Which makes sense, seeing as he's programmed to be stupid.
Papyrus from Undertale, when you first meet him. Unlike the Royal Guard, he's not actually out to kill the player character, but he still wants to run them through a gauntlet of puzzles before capturing them and sending them to King Asgore (who's killed six other children already). But he's not particularly good at it - with some covert help from his brother Sans, his puzzles become a non-issue, and the bars of his prison cell are wide enough to walk through (escape enough times and he'll ask you to let him know beforehand next time, because he got worried about you when you disappeared. And he means it). Averted, though, when his boss fight hits - first he drops the "ineffectual" part, then he decides to let the player character go, becoming a sweet and loyal friend for the rest of the game. The game strongly implies that he could be quite competent if he wanted to, but he's intentionally holding back because he only ever wanted friends and holds no malice towards humans whatsoever.
Team Skull in Pokémon Sun and Moon, especially in comparison to the evil teams in the past games. The only person who ever actually takes them seriously is Lillie, otherwise everyone dismisses them as a non-threat despite how much they try to be Gang Bangers. You even have the option to walk away from them during your first encounter with them! Of course, the team is mostly a front to distract everyone from the real villains who provide Team Skull's funding: the Aether Foundation and their president Lusamine, who are much more threatening.