I myself prefer 15" rims for anything up to a 35" tire, but I'm old... I think you can use 15s on a 3rd gen 4Runner but if you allready have 16s or 17s I would just go with it unless the tires are so expensive that it pays off to buy smaller rims.
I probably wouldn't stress out about a load range E tire being "stiff". Just remember that you don't have to run 120 psi just because the sidewall says you can. With vehicle appropriate tire preasure (maybe 30-35 psi for the road) you should still get a decent ride. There's nothing wrong with having good beefy carcasses.
On the mileage, it's been my experience that tread design and tire size will effect your mileage more than actual tire weight. Big lugs suck alot of power and gas because of rolling resistance. Mild AT tires will almost always fetch a mile or two per gallon better than a MT.
