Excellent finale - possibly the best of the recent TV season. BUT, here's what's bothering me, plot-wise... (spoilers for finale, obviously)
We know (by his actions) that Agent O'Loughlin (Van Pelt's fiancee) was a Red John mole and thus paid the price for messing with the head of a redhead by dying... in a hail of bullets from Van Pelt and Hightower! Quite right too! (Go, Rigsby!) It's possible other characters we know are also compromised (though I think LaRoche's secret is something different) but there's no direct evidence of this only the red herrings that play with the audience in the ep.
However Patrick and Co lure their boss Betram (who they think is the bad guy) to the shopping mall to hopefully also lure out his 'boss' Red John (it's only while they wait that Patrick twigs the reasoning behind thinking Bertram was the mole is flawed). So if Bertram IS innocent, why DOES Red John turn up at all - watch closely and you even see him arrive in the background near the very beginning of the scene? He shouldn't even know about the meeting unless Patrick and Co WERE right. O'Loughlin knew nothing of the meeting, so he couldn't have got the information from him. The only reason he'd be there is if he arbitrarily tailed Jane (far too convenient) or, most likely, knows about the meeting and that only works if Jane and Co were actually right about Bertram being the mole and their plan actually worked as planned. Or if one of the remaining members of the team is ALSO a mole.
Several people I know thought that the pendant O'Loughlin gave Van Pelt must have been bugged, but that makes no sense either as there's far too much information flying around earlier which would have compromised all the heroes' plans if they were being monitored.
It's a great dramatic finale and mucho fun, but this minor quibble makes no internal logic/sense to me on closer scrutiny...