But thats the whole point... its just stock. In the same way you said it, if you grab a stock Grand Cherokee or a stock SC Frontier (or Xterra) or a Tacoma, top of the line in their brands (cause you'd want the V8 Grand Cherokee just like you would the t4r) and you put a 2-3" lift, 33" tires with an aggressive tread and rear lockers then you're gonna be tuggin along well on any trail. (if you have tires that correspond to the trail ofcourse)
In my opinion, PURE PURE stock you're gonna be looking at the Rubicon and the H1 (for open terrain or very open trails... def not for the trails I run) would be the two I'd go with... definitely the Rubicon. But as with anything, I don't know if the Rubicon would last me what I'd want it to last without endless TLC.
The 4th Gens, as much as I hate to say it, wouldn't perform rough trails (that I try atleast) well unless you're alright with body damage and bottoming out often. Even with the skid plates, you do it enough and the reliability factor's out the door... and noone likes that loud clank that's made by bottoming out that makes the 'your wallet's shrinking' sound. Sport editions would do a little better because of the XREAS suspension with offroading in mind, in a sense, but the 9.1 inch (4WD) and 8.9 (2WD) doesn't compare with the 3rd or even earlier gen's ground clearance (nearly 2 inches higher for 3rd and 2nd gens= 20% higher).
And as I offroad more and more with my friends (in wooded and rocky terrain) (ignore this if you live in the desert), ground clearance and reliability is the biggest factor for stock trucks, save a locker or a winch persay. So yeah... the 4th gen might be able to make it up quicker and with more power, less RPMs and your ankle might feel less sore but you'd be clanking up the whole way (pure stock) and you might even get some nice little markings that tag your car as the 'Moron who Hit the Tree' offroader because of the 6 inches wider body, 6 inch longer wheelbase and 13 inch longer body.
I'd take the 3.4 2000 5 speed 4Runner with the specs you stated above over a 4th gen anyday, an Xterra (just for wheelin not actual daily life), wait for the FJ concept or a well kept FJ40 personally.
But hey... that's just my .02