It would help if you tell us which MODEL you're looking at...Trail Edition, SR5, Limited, etc..
A good compromise is the 2009 Trail Edition, which is a 4th gen 4runner and has the center differential along with A-TRAC and rear diff lock. So, IMHO, it is the best of both generations in a sort of way. The problem is that the 2009 TE is extremely hard to find...i posted one a few days ago with only 11k miles somewhere up northwest area...you can search for it if it interests you.