Well it's got to be either 1st gen or 3rd gen because that's what I have lol.
If you compare them both bone stock as they came from the factory, then:
- 1st gen '85 SR5 28" tires, open 4.10 diffs, 5spd, solid front axle.
- 3rd gen '99 SR5 Sport "Highlander" 31" tires, 4.30 diffs elocked rear, auto, IFS.
Advantage 3rd gen because of bigger tires and locked rear axle, and also the auto trans torque converter which adds an effective 2:1 crawl ratio. The stock travel SFA on the '85 is a little better at keeping both front tires on the ground than the '99's IFS but it's not enough to make up for everything else.
Adding: Another plus for the 3rd gen is a tighter turning radius than the 1st gen SFA. Approx 38' circle compared to about 40'. A little more maneuverable, which is nice.
I wheeled my '85 stock a bit but not for long because they are so easy and fun to mod and the payoff is great. To compare my mild built '85 to stock '99:
- 1st gen '85 SR5 32" tires, 5spd, diffs regeared 4.56, locked rear, LSD front, 2-3" lift flexy springs, crawler case
- 3rd gen '99 SR5 Sport "Highlander" 31" tires, 4.30 diffs rear locked, auto, IFS.
Now definite off-road advantage to the 1st gen. Of course there are lots of interesting places where they will both go, but then there are obstacles where I wouldn't take the 3rd gen and the '85 just walks up. It's frightening really lol.
On the street it is the other way around of course. The '85 was my daily driver for a long time and it's OK but the '99 is plush. Smooth V6, front and rear sway bars, ABS, air bags, cup holders, all the modern conveniences.