In my family, my wife and son prefer the 3rd gen. to the 4th. I drive the 4th as a daily driver and I find some good points to my 2004, but I will say my 2001 still is very special.
I like the front seats better in the 4th gen., also the ride and power. The extra trunk space and the quickness of the steering, you will miss if you leave the 3rd gen.
For me, I like them both, but the 3rd gen. is still very special, maybe it being my first 4Runner. If you click on my "Member's Picture Albums", you will see the two generations side by side.