With all due respect this is not true at all. I have an 05 LJ with 6 speed Manual, currently has 91K on it with absolutely no issues. In fact other than routine items my 05 has preformed perfectly and I only began to spend coin on it when I decided to install the OME lift.
Fair enough. Glad to hear that you haven't had any problems so far. I'm sure that with other known TJ issues, from the 0331 head to the PCM problems, the rate of failure is overstated on the forums. That said, there does seem to be a higher prevalence of problems—particularly popping out of gear— with that 6-speed transmission compared to the 5-speeds. At that end of the day it's all anecdotal, but if one were to choose which model Wrangler to buy solely based on preferring a manual, I think most would choose the 5-speed.