I had 2 JK Rubicon 2Dr manuals. Both hard tops. A 2011 (3.8L) and a 2012 (3.6L). Both were purchased used. 2011 was bone stock, 2012 ended up with 4.88s, 35s, small suspension lift, AEV front bumper with winch, yadayadayada.
I had no real issues with either. The 2012 did end up with a leaking slave cylinder for the clutch, which i fixed. Cheap part and was quick to repair. I'd have no issue owning another from a reliability standpoint.
I switched to the 4R mainly for drivability (much more comfortable. Wheeled the 2012 all over colorado and just kept seeing 4runners on the trails. Found out there was no need to beat myself crazy when a 4R gets along just fine), fuel mileage (LOL, it's bad when the 4R is considered economical), value and room (coulda gone to a 4dr JK, but no thanks).
Every vehicle has its weaknesses and the 4R is no different. I wish it was smaller outside, had less techy gizmos, came with better final drive ratios (4.1 or 4.33) and most of all...came in a manual transmission. But i've gotten by, i really enjoy it. But i also really liked my Jeeps too.