Speaking as someone who plays from the comics, I say go for it. Alternate universe shenanigans are part of what make a game like this so much fun. There might be a few people who would be like oh well it would've been cool to have X version of this character, but I think a lot of people would be thrilled to have that character to bounce theirs off of no matter what 'verse.

Out of curiosity, are you thinking of apping anyone, Anon? Or is this just an in general kind of a question?