Some fixes that, to me, would greatly improve the vehicle-

Make all the latest safety technology standard.
Better throttle response, quicker downshifting, top notch transmission.
More low end torque. Make it a pleasure to drive leisurely and not have to get on the gas so often to get it going.
Get rid of the nose dive.
Get rid of the clunk.
More driver's right knee leg room.
Much comfier seats.
Less exterior plastic cladding, streamline the car a bit with extensive wind tunnel testing.
Get scientific about dipping then factory coating the frame and underbody to prevent rust.
Maximize interior space and storage.
Better rearview and blind-spot visibility, more of a greenhouse feel.
More durable interior finishes.
Tighter turning radius.
Factory subwoofer and very good sound system standard.
Offer a manual transmission as an option.
Aim for 22 city 26 hwy mpg- I know that's a pipe dream. The new Rav4 is supposed to get 26/35 though so maybe there's room for improvement in the 4runner.

Bring back all the designers from the Lexus GX470 back and let them loose on a well thought out and seriously engineered reboot of the 4runner.

Bring back "Thundercloud" as a color option from the 3rd gen.