My list...
Some have been said already but I'll list them anyway:
1. Auto up windows. A bit of a PITA especially for the wife, who has a hard time when she just wants the window open partway. I'm also concerned about auto-up windows in general for safety reasons - kids and dogs, mostly (I'm guessing this is why most newer cars don't have the auto-up feature, at least not the cars I've seen.) I would have been happy to have auto up and down on the driver's window only.
2. FUEL GAUGE! I'm actually getting to the point where I just ignore the fuel gauge/warning light and use the trip meter as a gas gauge like I do on my motorcycles.
3. Okay, now I know this one is a really minor quibble, but I have to say it: Why is there a rear seat heater - but no rear- seat AC? Would it have been that hard to plumb the AC to the rear fan as well as the heat?
4. Visors. I miss the "extensions" that my '04 Taco had. May have to retrofit some Taco visors.
5. I find the 3.4/auto combo has adequate power (not great, but adequate) but the MPG kind of sucks for a vehicle that is this lacking in power.
6. Along with #5, the poor MPG combined with the stingy 18.5 gallon gas tank gives the 4runner a really limited range. Practical range in city driving is ~250 miles. Even for the highway, you've got to figure on 300 miles maximum safe range. OTOH, my 90 Montero could go 400+ miles on a tank (thanks to its enormous 24.5 gallon tank) and even my little '99 Subaru could go nearly 400 on 16.5 gallons on the freeway.
Having said all that...the "pluses" of a 3rd gen 4runner are so numerous that they more than overcome the little nagging "minuses."
The fact that out of the box, with no mods, my 4runner can run 4 - 5 rated trails (on the 1-10 scale used by Traildamage.com) with no difficulty, fit 32" tires with no suspension mods, has a rear locker from the factory, and is reliable enough to drive anywhere even with >125,000 miles on the clock means that the 4runner is by far the best vehicle I have ever owned!
And when it's finally time to trade it in, it will almost certainly be for another 4runner!