tradeoffs in them all...
1998-99 2 pinion diff and rear locker
2000+ beginning of 4 pinion diff but some (few) have had tranny problems but ATRAC is outstanding as is VSC; 4 speed tranny
2003 got more horsepower and 5speed tranny with lots of other upgrads such as steering, stronger u-joints, better driveshafts, no contact throttle position sensor, etc....
If you dont mind having Nav-HVAC-RADIO all built into one unit that also fails..I would say the 2003 is best bet for upgraded configurations, better systems, etc...minus the head unit for NAV-RADIO-HVAC.
If that is a little too steep for you I would go for the 2002 model that had no real changes from 2001...but they had two years to get it right.....and three years on the tranny to work out bugs and other things found. I would say late 2002 or the 2003 is best all around depending on how much of a deal breaker the Nav unit display is since it is not replaceable with aftermarket systems if it fails....for that reason I would go 2002...but that 5 speed would be nice. It is a tradeoff....
Standard head unit that can be replaced with new aftermarket but only have 4 speed.......or 5speed tranny with lots of drivetrain changes for better...but roll dice on head unit.
The holy grail would be a 2003 without the Navigation system....now that is the TICKET! If you can find one....
Just my two cents.
That being said I love my 2000.......blew front diff on 4 pinion....and either way it is upgradeable with ARB or aftermarket gears if it blows and gives you excuse to also change gearing if you go for larger tires.

If tranny blows...rebuild it or buy a refurbished one and drop it in for antoher 150,000-200,000 more miles.....any choice is good...just depends on your tradeoffs.