I have an 05 with the 6 and auto transmission.
The engine is fantastic, but I've heard rumors that the transmission is the weak link. I put an external cooler on transmssion, and I still see high temps when offroading - I think at the end of the day these transmissions weren't made to be run in 4wd for hours at a time.
After saying all this, I've got 115K on it, and haven't had a single engine or transmission issue.
Coming from a YJ, the main thing you may be surprised by is death wobble. If the new Jeep has a worn suspension that could be a real possibility. I would suggest test driving it on the highway around 60mph - the bumpier road the better.