Maybe this is the moment to ask why Hermione isn't already the hero of HP:MOR. If the point of HP:MOR is that someone who is smart and rational (and raised by smart/rational muggles) would immediately find a million holes in the Potter-verse, why not start with the character who is already known to be the smart one, and is at least a bit more rational than canon Harry? Sure, there's some issues with the prophesies -- but (rot13 for spoiler) Hayhaqha had a pretty good solution to that.