The 3.6 seems to get better reviews than the earlier 3.8 as far as performance but I'm not convinced that the 3.8 is bad at all from guys I know that have had them. There are a variety of problems with the 3.6, problems already mentioned but the worst I think are some doomed valve train / head failures of some possibly due to casting / initial cleaning issues. Story seems to go that these failures usually occur sooner than later destroy one head and valve train [left?] but not too common and many were covered by warranty.
The 3.6 from 2012 to about 2018 is changed for 2019 and I think some weight is shaved through thinner casting walls and I think low rpm torque is addressed.
The 2012 3.6 is a 60 degree even firing VVT engine and after 2018 may be VVT / VVL.
The Penstar 3.6 is widely used in many different vehicles and had millions of test miles done by [can't remember the name of the race team / company, did the '64 Hemi if I'm not mistaken] during the course of development. I believe they're nearly the template for modern V6 engines.
My 2012 is the standard 6 speed NSG370 which I had to rebuild because of failure of the second gear engagement teeth / shift collar. My shifter and fork assembly were in good condition but at only 115,000 km the clutch disc was near the rivets. The flywheel which has a contoured surface and can't really be machined cleaned up well. Bearings, seals, 2nd and reverse gears, synchros made an inexpensive rebuild, but if someone had bashed the fork assembly or cooked the flywheel would have doubled / trippled the cost.
Many complaints about the factory clutch being too weak or failing; 275 hp and an 11" clutch so I thought that was BS, I installed a cheap kit.
After 2018 I think they go to the dual clutch which is a recall problem with some odd 75,000 units affected and a stop on delivery of new Jeeps until a remedy was determined. It seems that if the clutch was failing or overheating it could reach 5,000 degrees or so, disintegrate and splash through the newly thinned out transmission casting and passenger compartment.
Mine has probably the lowest available factory gear ratio and stock 18" wheels without any mods. The combination of non predicatable / repeatable rpm vs accelerator position inherent with the drive by wire combined with lousy torque below about 1,900 rpm and living on a hill [and maybe not being the driver...] makes clutch wear and tear a maintenance fact of life in my case but I know of a couple flat earth people that have 200,000 km on the original clutch.
Also, the ebrake, well, that just doesn't work; when I initially bought it I replaced the rear disc / drums along with new pads and [ebrake] shoes. Still couldn't hold on any significant grade.
So... get an automatic
On the plus side, they're well engineered and built, the engine is awesome [over 1,800 rpm] once you rev it up, great on the highway, transfer case is great, unstoppable in snow [what I bought if for] and [for now anyway] the transmission and clutch work perfectly, very happy with it and no regrets.