When the 4th gen 4Runner's came out, I test drove the first one my Dealership received. Some of the subjective things I didn't like, were no available manual transmission, and the flat-top wheel wells that reminded me of a Jeep Grand Cherokee.
What I couldn't live with, was the lack of headroom compared to my 3rd gen.
The headroom issue was fixed in the 5th gen, but still no available manual trans. At this point in time, my interest in buying a new 4Runner isn't what it was back in '03.
So I still have my '97 SR5, 4wd, V6, 5-speed, Factory Leather, moonroof, and E-locker equipped 4Runner, that runs as good as the day I drove it off the lot almost 17 years ago.
Test drive both, and decide which you like best.