I think if ANYONE would react poorly to having characters from their IP's used it'd be Nintendo. Otherwise I don't think any fighting game company would care too much so long as you're not making money off of it.
Ermac and Reptile are in need of new ideas but they will happen. Also I wouldn't use Chucho's They aren't quite up to par with what would be needed to match Sean's style. This is all quite theoretical though. Sean's game is good as is though.