The fact that Patrick Jane could be Red John just seriously ruined my day. Mostly because it makes way too much sense. I would be incredibly disappointed if PJ was RJ, so this is a defense rather than an accusation 

1) Dis-Associative Disorder people have no knowledge of their counterpart. If Jane had a second personality, there would certainly be times when he returned to himself in situations or places he could not remember. Red John would have no knowledge of being Jane, and, therefore, would not have the foresight to return to where Jane had been or change back into the three part suit (if he wore something else) before the Jane persona came around. The show would have made hints to that end.  

2) Red John's accomplices are not that sophisticated. In season 1, Red John's Footsteps, both Rosalind Harker and Sheriff Hardy know Red John personally. If my first point was correct, than Red John would have no way of warning them that his other personality would be coming by to investigate. Realistically, Rosalind and Hardy would be very surprised to have Patrick Jane who is also Red John on their tails (the episode also gave the impression that Red John was watching Jane and Lisbon from a separate place). I can't remember the accomplices or situations from later seasons, but I think the concept applies to the the others too. 

3) How could one person save himself? In the season 2 finale, when Jane is at the mercy of RJ imitators, he is saved by Red John personally. An argument could be made for another accomplice, but I'm pretty sure that was supposed to be RJ himself. 

4) I don't think Jane had the time to commit several of those murders. Split personalities or not. Perhaps they were always accomplices, but really? More accomplices? Red John is a serial killer because he likes to kill, not delegate. 

I'll have to go through the previous seasons again, but this is what I've come up with so far. If anyone can explain one of those points, that would be fantastic.