I just switched from a 99 trooper to a 4runner, but I haven't sold the trooper yet. Still drive it occasionally.
I've wanted a 4runner for a long time, but those troopers are very nice. Tons of interior room, and the hidden compartment under the rear seat is just cool. And useful.
The trooper seemed under-powered to me. Sluggish, and my mpg was terrible.
The 4wd system is actually really good. Someone said it earlier - that 99 trooper will walk through things that most other stock 4x4s will not. Many have limited slips in the rear.
Troopers are known to burn oil, mine did. Don't let that scare you. Switch to manual hubs first. I would also upgrade the intake and exhaust. That motor performs better when it breathes better. Oh, and the headlights suck. Terribly. Upgrade the bulbs and you'll want to add a decent set of fogs.
Congrats on the purchase!