PJ is RJ in one sense but not the other no pun intended.  PJ throughout having a troubled familiy life and other issues suffers from an undiagnosed case of multi personality disorder. ANd how it has gone undiagnosed for so long is due to his mentalist abilities are accessible by both personalities that of PJ and that of RJ. 

In essence Patrick is chasing his other personality the sick side of Red John but unaware of it. Using his mentalist abilities to have others unaware that they are doing and committing many of the acts for him Red John while under his mentalist influence.

Now will the final episode have Patrick jane in an alley questioning a gang member where Jane sees a reflection off a car window of him self but to his surprise for a moment the evil personality display itself (RJ)  at that point does Jane grab the gun of the gang member and start shooting at the reflection. Only to startle other nearby gang members who shoot and kill Jane along with injuring the gang member Jane was talking with  When police show up they find that a person limped away leaving a minor blood trail and find Jane dead on the ground with a little blood happy face drawn on the ground by Jane before he died. And no gun to be found.   The authorities leave the case open thinking red john killed Patrick Jane and never known they misinterupted the final crime scene.  PJ & RJ both go to the grave only knowing the truth. The end.