RE: Homestuck (and other non-anime) cosplayers
Fandom should be fun. Cosplay is part of fandom. It should be fun. You don't find Homestuck cosplay to be fun? Nobody is making you cosplay it, or take pictures of it. They paid for a badge just like you did, and presumably they are spending money in the dealer's hall and artist alley, just like you did; and they are participating in the convention, just like you did.
Honestly, I have zero interest in Homestuck myself, but it sure as hell isn't my place to say "You can't dress up at a convention the way you want." (Provided, of course, that said costume isn't violating any public decency laws or convention guidelines.) And frankly, I would think very poorly of Fanime's management if they tried to enforce an anime-only cosplay policy. There is a TON of overlap between anime fandom and various web, comics, and video game fandoms. People like to dress up to reflect one or more of their favorite interests, regardless whether it's Fanime, Anime Expo, or Comic Con. It's no different from the huge cosplay fads for Bleach or Naruto or whatever other fads have come through. It will flare up for a few years, then taper off to less blatantly visible levels.
And having helped run even a small convention, let me tell you: It's very easy to say "Hey, you should set up your own convention for X thing!" Actually doing so is a very large, very expensive logistical undertaking that requires the cooperation and lots of donated time by a large group of people. You have to consider venue, organization, safety (and insurance liability,) staff and organization... and none of these things are particularly cheap nor quick and simple to do.
I suppose the tl;dr version of what I'm saying is "You just gotta deal with it!" Getting worked up about what somebody else wants to wear for a costume is just absurd.