I think aside from Ninjara, the characters commonly discussed as alts could use basically the same animations without much of an issue. Byleth (and probably others that I don't remember) already features different idle animations and such, so I think slightly different animations could be done, without affecting hitboxes and the like. As for Ninjara, yeah, that might mean he doesn't do things as ninja-like, but not to an egregious extent, honestly. Thems the blows, I guess.
These discussions are really hard to have because they basically hinge on what each of us has in our mind's eye, and that's hard to convey for obvious reasons. For the talented people in the community, a mock-up could be made, but I'm certainly not one of those.