Bowser, Bowser Jr., Ganondorf, Andross, K. Rool, Dark Samus, Ridley, Mewtwo (kinda) to name a few. There are many other villains too, but like you said they aren't very major and appear in like one game in their series.

People keep asking for WW Link.

I want Majora's Mask Link. Now THAT would be an interesting moveset.

http://www.serebii.net/index2.shtml

Jigglypuff is returning...PLUS, a new character appears for the Pokemon side! It's LUCARIO!! Look on the Serebii website's front page and click the spoiler icon. It will tell and show you that Lucario and Jigglypuff are in the game as playable characters.

Also, looking back, I was surprised that there were only 3 playable villains in Melee.

At least there will be many bosses in SSE to fill the void, and we already have Wario and kind-of MetaKnight and DDD as villains.

Old News Naraku...

Metaknight isn't a villain. He's just Kirby's Rival. I believe in Kirby's dreamland he kept part of the Star Rod so Kirby can't put it back together because Metaknight knew Nightmare will come out.....Nightmare for Brawl!!!!!

Yeah. Quite honestly the only villain that feels to me like a really great badass villain is Ganandorf (Bowser, for instance feels like a poor goofy guy destined to try ridicullous plans to kidnap peach (which is not a bad thing, I love that goofiness), while say Dark Samus has some limitations for being just a dark version of the hero (I only played Prime 3, maybe I would think otherwise if I had played the first ones), and Ridley isn´t a true evil master per se. As for Andross I unfortunately never played any Fox game. And Mewtwo like you noticed can´t be properly considered like a villain). 

Bumped from 5 pages ago.

Just so people don't forget....

Also, for those of you who may have missed the news. 

I know they are rivals. That is why I said 'kind of'.

I guess the proper term is more of a foe than a villain.

@Grupoid

You have to admit, though, Giga Bowser is badass. Bowser in general has an edgier look this time around.