I wanted to go back and watch old episodes for clues to who should have been red john. But i just realised, that there's no sense at all in that.
None of the clues add up. I think Heller was so busy giving us Red Herrings, that he forgot to acctually create a real background for Red John.

In my humble opinion Thomas Carter was a far better choice for Red John than McAllister. But why the hell are both of them named Thomas?