The need for rationalization on this subject is pretty astounding, gotta say. I clearly didn't hate it as much as some people, but I don't find myself grasping for a completely unassuming character to be the "real" Moriarty on the grounds that who we got wasn't who we expected (with reference to how he was played & characterized, not that we didn't see who Moriarty was from a mile away). Molly is who she is unless she's a really great actress who's been able to fool Sherlock for months or years. I doubt that.

Molly-as-Moriarty is great crackfic material, though XD