The 3rd gen offers better stock clearance while the 4th has a bunch of gizmos (Hill Assist, DAC, VSC) that may or may not be useful. I cannot offer much comparison between the 4wd systems, however. The 3rd is also lighter, shorter, and narrower -- always a good thing IMO.
The one thing I hate about the 4th gen is the poor visibility out the windshield on hills. The front of the hood is so high, especially with the silly SE hood scoop, that you frankly cannot see a damn thing sometimes. I even managed to run over some tools on my garage floor because I enter up a hill and can see nothing but the roof of the garage until it's too late. I'm not saying other trucks have great visibility going up hills either, but I just feel like the 4runner is one of the worst I've experienced.
