I own both so here is what I notice.
No soft close tail gate on the 5th gen.
No burger tray on 5th gen.
Pain in the ass to change oil on 5th gen compared to my V6 4th gen.
5th gen is heavier and actually feels a little slower.
Non matching spare wheel on 5th gen.
Much better ride from the factory on 5th gen vs 4th gen
Much better insolation from road noise on 5th gen.
Switches, instrument cluster and controls better lit on 5th gen.
The TE has a real transfer case shifter.
The interior is much nicer all around on my TE vs my 4th gen SR5
5th gen is a little bigger all around and feels like a bigger vehicle.
Those are just some things that come to my mind right now. There is probably much that I missed. Overall, I really like my TE. Since July I have put 10k miles on it. Very comfortable, even on long trips. I do wish my 5th gen had more power though. A V8 option or supercharger would be nice. That being said, the transmission does a good job of making up for the slight lack of engine power. This newer version of the 1GR-FE V6 in the 5th gen feels like it wants to stay at the upper end of the RPM specture much more than my 4th gen. On the freeways in CO, going through some mountain passes, my 5th gen had no trouble keeping speed though. I do get about the same mileage in both 4runners though, roughly 19 mpg.