For a Naruto fan to even remotely accept the theory of Shino being the leader of Akatsuki, it would take a manga creator skilled enough to make such a plot twist believable.
These are skills that Kishimoto obviously does -not- have, so if Shino indeed turns out to be this mystery man that even Itachi seems to fear (which he won't); it will only be awkward if Kishi tries to pull it off.

I think it's quite safe to assume that Akatsuki's leader is yet another entirely new character, though I'd like for at least one of the unrevealed members to have a relation to an established character (imagine one of them being Rin - that would own).