The problems on the '05-'06 models are hugely overblown IMO. I have an '05 LJR which BTW did not exist before '05.
Replacing the OPDA is pretty cheap and painless as long as it's done before any significant cam damage. I replaced mine at around the 85K miles. It was throwing codes because the OEM assembly was worn but cam was O.K. No codes after replacement of the OPDA assembly but retained an original OEM sensor.
I also replaced my PCM just recently with around 130K miles on it. It did not completely fail but began to show symptoms (engine dying, gauges erratic, etc.). I don't think PCM failures are unique to '05-'06. But
@Wranglerfix can confirm or correct that statement.
Basically, there are no issues on the '05-'06 models that cannot be resolved fairly easily. There are surely a few haters of the '05-'06 years but many of the haters have never actually owned one. I'm happy to have an LJR with a manual transmission, not available before '05.