Power Antenna Broke, and I had to dig nylon pieces out of the motor prior to replacement which means removal of said motor. Suggest replacement of unbroken antenna mast (easy task) every 2-3 years.
Front brakes and rotors had to be replaced at around 40,000 miles. They developed a small vibration that quickly grew to a steering wheel shaker. The replacements have lasted until now (86,000) without a problem even with no change in driving styles.
Significant rust on inside of chrome bumpers. Toyota doesn't seem to worry about adding decent corrosion protection here. Perhaps it's because the rust won't make it through to the chromed side for years, and the owner will forgive them based on age. Considering the excellent nature of the rest of the design and build, why did they choke here?
Lots of plastic pops sourced from the stock radio/6 disk changer. This can be from thermal expansion, bumps, or simply pushing the buttons. The rest of the car is silent, so this noise factory really stands out.
AC Weak. Everything in order, but it just seems weaker than most other cars.
Fuel tank too small. With my GMs, you're generally good for over 400 miles, but with the 4runner you're on fumes around 310-320.
Sunroof can rattle if stopped at certain points in its tracks.
Speakers are weak, even with the better stock sound system. Sure, they can get loud, but the sound is not that rich.
Power level is merely adequate. The 3.4 doesn't feel powerful, nor can it accelerate quickly. This is not critical in a vehicle of this type, but I'm sure it's led to the disappointment of more than one buyer.
Windshield seems more prone to rock chips than any other vehicle I've ever owned.
I'm a real critic so the above issues do not detract from the fact that this may just be the finest automobile ever produced.
Like it or not, all cars are machines, and machines need maintenance and contain wearable parts. When you add to this, the drive among manufacturers to lower production costs by reducing the quality of components, the '99 4Runner really stands out as a winner. It has the build and parts quality (minus the CD changer and Antenna) of a much more expensive car.
I purchased my 4Runner in excellent condition on the used market with 9,000 miles on the odometer, and 5 years and 75,000 miles later it's almost in the same condition as it was when I bought it (minus the bumper issue above).
Best feature? The power rear hatch window. It's down at least half of the year...