I'll be the first to admit that I have a complex little network of mental filters when it comes to deciding if I'm going to write a story idea or let it die in bad-plotbunny-hell. However, those filters deal with concepts and events and whatnot, rather than pairings. When it comes to pairings, I'll tend to write whatever I like, regardless of popularity.

I can't speak well for HP, because I've written very little so far, and it's not been rarepairs. In my other fandom, though, some of the people I write, general fans haven't even really heard of. If those aren't rarepairs, I don't know what are. *g* Still, though, I've never particularly gotten wild amounts of feedback in any fandom, so I don't necessarily notice much of a difference.

Though, I do tend to blame a complete lack of feedback, which happens occasionally, on shoddy writing skills when it's my own work.