How many miles are on your transmissions?
I can tell you the previous owner didn't know how to drive, or didn't understand the basic principles of a truck transmission. My NSG370 only had 55k miles on it before the reverse gear was shot, 1st gear was incredibly hard to get into, etc. (that's how I bought it). I replaced the entire thing with a rebuilt unit and I am very particular on how I drive now. I won't even let my wife drive the Jeep because of it. Regardless, a lot of people abused the shit out of these things and that's why people think they suck.
Mine has 128k now, had 119k when I bought it and I inherited the problem. I don't know it's history but everything else on the Jeep was in a better state of maintenance than the 99 TJ I had before that, which had 116k on an Ax15 that was quiet, tight, shifted fine into every gear and stayed in, so I have no reason to believe the nsg370 was abused any more than my Ax15 was, and in fact on the first oil change the Ax15 came out looking like it had water in it and the nsg370 came out clear with a caramel color (I acknowledge the possibility that someone changed the oil before the sale, but the lubricants in all the other gearboxes were not overly used but certainly not new...maybe he changed it hoping to fix it)
I doubt that 05-06 TJs are somehow on average more exposed to abuse and neglect than 97-99 or 00-04 are.