Had a 2003 Sport before my 2011 SR5.
2003: Miss the Center diff, shift knob, seat fabric/padding(side of my drivers seat is completely crunched), more defined shifts and I perceived better on road manners(maybe it's just me). Overall, I felt the powerband and shifting suited the vehicle better than the 5th gen. On road and for a daily driver, I liked this 4Runner more.
2011: Love the manual mode on the tranny, and the ATRAC comes in really handy off road. I like the fit and finish and the offroad ability of this 4Runner more.
However, since I'm on road 90% of the time and given the road conditions here during the winter, I'd really like to have the ability to drive around all day without shifting in and out of 4hi. Hence, I'd probably trade ATRAC for a center diff if I really had to choose. I realize this is possible with the Limited, I'm just not a fan and couldn't justify the additional cost if even if I was.