MUGEN itself is obsolete and illegal to distribute, actually. Elecbyte has said they're making a new version, but there's been no word for 2 months or so.
Mugen Fury - Créez votre propre jeu de combat 2d avec MUGEN for other, more updated ones.
I am also making a 3D fighting game, and intend to stick to clean OO style internally ... I may release the engine at some point.