Although in the latest episode it was a little TOO obvious that the big assassin guy was not the real Moriarty-- and it should have been to Sherlock as well.
How would it have been obvious to him? He didn't yet know that there was
a Moriarty, so he had nothing to compare the guy to. He hadn't even heard the name Moriarty until Moran told it to him -- he just thought he was going after a serial killer called "M."
I guess what's unusual here is that we're used to seeing the character of Moriarty introduced at a point when Holmes is already aware of him and has been tracking him for some time -- but here we're coming in on the ground floor, seeing the moment when Holmes first became aware of a shadowy criminal mastermind.