I see nothing wrong with cosplaying unknown/unpopular characters if that is what you really want. I personally don't go by what is or isn't popular, but what I like. As long as you are having fun and enjoying it, that's what really matters.
I have a feeling that if I finish my costume and able to make it to Anime Expo, I will probably one of the only Trauma Center cosplayers there (there might be a few others, but fandom is kind of small). Either way it's cool.