Buso Renkin
Would Final Fantasy count? I mean, it went from RPG to Shooter with Dirge, and I never played Crisis Core. Personally I think Dissidia just does not cut it. I want to see Vincent vs Sin. Idk, a doujin fighter with every character from every game would be awesome.
Naruto needs a GOOD 2D Fighter.
NGEvangelion. Mech battle fighters are cool.
Baki would be cool.
Berserk if Guts wasn't playable lol.
Trigun
Outlaw star
A tenchi muyo fighter. It could be, "Tenchi: All fight for Tenchi!!" and all the female cast are playable, and the storyline is they're holding a tournament and winner marries Tenchi. Could totally work.
Kikaider. I would love to play it.
Ninja scroll fighter would be cool.
Not really an anime... well I guess Z, but Power Puff Girls. If there was a good fighter for this, I'd be playing it constantly.
Alright, I think I named enough. I also named so many anime because fighters aren't hard to make in all honesty.