I voted for two awards not because I consider male vs. female character writing to be different disciplines, but because I would like this award to be about fun and awesome characters. For example, some people might consider The Terminator to be a really interesting character, even though the movies would never win one of the more serious "best screenplay" type of awards. Some characters are just really cool, and this is a chance to recognize them. So while we're at it, why not two, just for extra fun? Though I admit the point about missing the non-gender or otherly-gender characters is a fair one.
Also, it might be kinda fun, in a presentation kind of way, to give the award to the winning characters, instead of the creators.