Personally, I think that changing the order now -- thus attributing to it an importance it never had before -- would pretty much guarantee that anyone not listed first would feel unwelcome, so I don't think it would be a good idea.

Right now, I don't see any significance to the ordering. RPS gets listed last among the fic categories, even below het and "other," yet I doubt anyone could claim that RPS is unwelcome or unpopular in the fandom. As a gen fan, I really couldn't care less what the order is. It's certainly never been a factor in whether or not I feel welcome in the fandom (which, for the record, I do).