I don't even need to say much because most of the villains I fucking love were already listed above for me, but I'll go anyway.
Metal Face: Holy hell this is one of the best baddies in the history of ever. Like when I figured out he was in Smash I screamed like a little girl. Everything about him is perfect. The weird thing about Xenoblade is that most of the characters and plot elements in the game are cliche, but the game does all of the cliches right so it doesn't even feel like it's worn out. Like Metal Face is pretty generic at the core down to his generic evil voice (which is one of his best aspects), but he still ends up being amazing. I was only disappointed that he didn't get more screen-time. Like I understand how the game's plot progresses Metal Face can't be the main antagonist, but I just wish he showed up more. Then again, he shows up a lot. You do fight him like 4 times after all. And the cool thing is that every fight is unique so it doesn't feel like you're fighting the same boss every time. And you hate his guts too. Like he's definitely one of the most hate-able villain I've ever seen if not the most. You legit want to tear him to tiny shreds just like Shulk does.
Ghirahim: I don't think I should add anything because I have nothing to add that others haven't said already. He's just one of my favs.
Solidus Snake: This is a pretty unpopular opinion, but here it goes: Fuck the final bosses to MGS3 and MGS4, MGS2 had the best out of all of them. Alright, I may be exaggerating, but this is a severely underrated battle in my opinion. I don't know if I prefer it to MGS4, but it's damn good. The cutscene that plays before it is mind-boggling and the birds flying up in the background as father and son prepare to fight to death with swords, I can't help but feel chills. Everything about it is perfect and the the end to it is sooooo satisfying. Solidus Snake is best Snake. Liquid's a whiny little bitch.
Dimentio:
For anyone who's even played Super Paper Mario Dimentio is probably on their top 10 list of game bad guys without a doubt, and there's many good reasons why. For one, his quotes. People think Fawful was a gold mine but goddamn Dimentio.
Example: "Your blows are like tiny jackhammers wielded by tiny, angry road workers!"
And he's not all fun and games too. He's pretty evil too in what he does as well. Just quotes alone wouldn't be enough to make him as memorable as he is.
Dark Samus:
Everything from her design down to her actions makes Dark Samus amazing, and she never utters a word throughout two games. Her actions are all she really needs. In Dark Sammy's first appearance she doesn't do much, but her appearances are definitely the best parts of the game, especially the final battle. In the 2nd game, her presence is felt throughout the entire plot down to the end. In the first game Dark Samus just seems like some neutral and mindless force that gets in your way, but in this game, she is the embodiment of everything that is evil. She forces you to kill everyone you know and profits from it. Just like Metal Face, you really want this bitch dead.