Someone made game with Metroid Fusion sprites years ago but the project died. Some OpenBoR games have Samus Aran as playable also.
But in general, it' s possible to create metroidvania with OpenBoR and I've made some of those.
Not quite a "franchise" per se but I wanna see someone make something similar to Crazy Zombie, a flash game that's a wave-based beat em up using sprites from MUGEN.