Ultimately, it was reliability "issues." Since just about day 1, the manual transmission made a sound a bit like a coffee grinder in 3rd and 4th. It was a sound that not everyone could hear, but I could both hear it and feel the vibration. They replaced the top shift mechanism, transmission, etc. over several long trips to the dealership. They also had a regional tech specialist spend a couple of days with it. Poor thing was taken apart so many times, but they could never figure it out. Ultimately, I was told by Jeep that some manual Wranglers do it, and some don't - and the forums are thick with those who have had similar problems. No, all that said, it wasn't a major mechanical issue, or so I was told...but, I'm a bit OCD, to put it lightly. Each time I drove the thing, I would obsess over the sounds and vibration and grind my teeth in anguish. Sadly, that's not an overstatement. I just didn't feel comfortable keeping a vehicle that was giving me such heartache with less than 15k miles.
I think it is important to note that the vehicle I had just before the Jeep was an '03 LR Discovery, which gave me more than it's fair share of heartache. I wasn't willing to suffer problems with a new vehicle; I wanted peace of mind.
So, I was looking a lot at Tacomas when I bought the Jeep, and decided that would probably suit me better. I sold the Jeep (with a lot of limited warranty left, and even 100k powertrain) and bought the little truck. I'm thankful I made the switch - it's refreshing to not have a sore jaw just from driving to work and back, fretting over coffee-grinder sounds. Now I just need to fix my OCD.