Great finale with a lot of material for the next season!
I don't take for granted the man killed by Patrick is the real or the only Red John. Neither do I take for granted that Craig O'Laughlin is the only mole. In both cases, there may be other ones.
All Red John's agents either are killed or commit suicide: they're disposable. Do you remember the connection between Red John and the cult leader Bert Stiles? On Season 3, Episode 3 - The Blood On His Hands, Bert Stiles gave Jane information on Red John.
The rope left at the hotel room may be long enough to climb down to lower levels (not just the one below) at the hotel. Patrick though he had the advantage, but he lost his analytical skills on that moment. So he might have been played and fooled.
And the presumed assassin killed herself to avoid leaving any clues, as the suspect was killed by J.J. LaRoche. What's the dirty secret on LaRoche box on the safe?
So next season may be really exciting, with Red John's ghost still alive!