(Quick Note: DO NOT EVERY GOOGLE "PHOENIX WRIGHT AND MILES EDGEWORTH." Just don't do it. Just never ever ever do it. Please.)
Among the first maleficent public servants to face Wright's zealous OBJECTION's is Miles Edgeworth. Though friends as youngsters, Edgeworth and Wright initially have very different takes on the proper course of justice - for instance, one's a prosecutor and the other is a defense attorney (and an ace one at that!). While Miles is not evil or corrupt like some of his associates in later entries, his desire for victory at all costs makes him a ruthless adversary. Also, he dresses like Liberace. Eventually though, Edgeworth decides being bad ain't so good for the win record - and he ends up siding with Wright on several cases. Unlike many of the villains in Ace Attorney, Edgeworth's transformation over the series has been more permanent and he has even starred as the hero of his own titles. It's arguable if he is even a villain anymore - though he still wears frilly clothes, proving that at least he still has bad taste.
Most of the teaming up with a renowned scoundrel packs a punch because of the usual history of animosity between the two characters. But in this case, the villain doesn't really know you that well - she just hates everybody equally. Then she gets to know you over the course the game. And still pretty much loathes you just as much as before. Perhaps it was something you said? Still, with both your backs against the bloodstained walls of the Von Braun, you two have no choice but to try and work together. "Working together" in this case means SHODAN orders you to do something and you do it. And then after you do it, SHODAN says something spiteful. Then again, it's a method that gets results - perhaps proving that tough love (or no love at all) is a terrific motivator. Perhaps the world's evil stepmothers are on to something. Valid counterpoint: You both end up trying to murder each other.
One of the most classic hero/villain pairings of videogame history is the endless war between a portly Italian plumber and a giant turtle king. Despite all the well-armed minions, elaborate castles, and fleets of airships (Bowser is either secretly a very capable ruler able to rebuild a vast empire in a jiffy or has very good accountants), the Koopa king's one goal of finding a mother for his ever-growing brood of adopted, eternally youthful children is always upset by the intervention of the Mario Brothers. And that's how it goes, again and again for all eternity. It's not a Mario game unless these two are facing off. Unless you count the games where they don't face off. In Super Mario RPG, the heinous highness is forced to aid Mario against their common enemy: an extra-dimensional robot blacksmith. Keep in mind this is a world where eating mushrooms grants special powers, so pretty much anything goes. Unlike the bouncy Mario, Bowser doesn't need to engage in raccoon cosplay or try magic fungus to give him an edge. He's a powerhouse of monstrous strength capable crushing anything into meat jelly... except Mario of course. Never Mario. Now if only those two would just work together more often just think of what they accomplish - there would probably be a castle surplus for one.
Chell isn't much of a talker (though to be fair that could just be the result of brain damage induced by prolonged stays in various stasis chambers). Luckily, arch-nemesis/evil computer GLaDOS is happy to speak for both of them and even happier to subject Chell to a series of grueling tests meant to ultimately culminate in her death. Unfortunately for GLaDOS, Chell is the one human its encountered who is bad at the dying part. (One might think just locking her in a room with no portal-worthy walls and no exit might have worked since it has the ability to alter the facility's layout at will... but I'm sure there's a very science-y reason for not doing that.) But they are forced to put aside those differences when seemingly benign blockhead AI Wheatley takes control of the facility, gains a mean God Complex, and condemns them both to the abandoned caverns below. Forced into the body of a potato, GLaDOS is not able to offer much in this new partnership aside from some advice about puzzles and one-sided conversation (again, it's a potato). But it makes up for that by rescuing the facility from an explosive meltdown and finally freeing your character - though for all we know in the time Chell's been in stasis the world has become a hostile wasteland full of exotic predators who don't turn off after being flipped over. So, I guess hate really wins out on this one.