I have a 3rd gen SR5 and a 4th gen SR5 (both V6s, both 4WD).
The 3rd gen 4Runner is an excellent truck (you'll love it), and the 4WD is fantastic. The 4th gen is even better.
Power: 4th gen has more power (duh, it's a bigger engine).
Brakes: 4th gen has better brake feel IMO.
Comfort: 4th has rear seat vent for fan and a/c...3rd doesn't.
Handling: 4th is both more compliant and has less body roll and "slosh" when you turn. I know that doesn't make sense, but somehow magically it has both (those little Toyota engineers are geniuses).
In the 4th gen, the V6 is plenty powerful for my needs. The V8 would be a waste for me.