If I were in the market for another 3rd gen I would just get the cleanest one I could find regardless of year. I would skip the 1996 model year as they aren't as supercharger-friendly and the 96s are not CARB approved with the supercharger if you live in California. (Obviously not important if you don't plan to supercharge.) The headlights, center console, etc can all be upgraded easily. Two small things that cannot be easily upgraded are the LCD odometers in the 99+ models and the climate control in the newer Limiteds.

I prefer the 99-00 model years due to the availability of a manual transmission and the locking rear diff, both of which ceased production in 2001. 01 models did at least gain ATRAC and multi-mode.

If you compare my e-locked '00 to an A-Trac equipped 01 and you handed it to the average person that knew nothing about 4WD systems, I think someone would get further offroad in the 01 due to the automatic ATrac system. However if you know about the e-locker and what it does, the 00 would get you further.