Auto Climate Control
This gets my vote as the least desirable feature on our '03 Limited. In the summer, it insists on switching into recirculate mode when the cabin temp is above ambient, even if the A/C compressor is turned off. And this behavior can't be disabled by switching to manual mode!
In auto mode, it defaults to having the A/C compressor running at all times, even in the winter when ambient temps are in the teens! At least, the compressor can be manually turned off while the system remains in auto mode.
I'm reasonably pleased with the system's cold-weather auto mode performance, and generally leave it on. However, the auto mode's choices of fan speed, recirculate and air outlets are just plain bizarre in hot weather, and I keep it in manual mode during the summer.
IMHO, this feature should be completely redesigned. For an example of a good-working auto climate control, Toyota should test a BMW 5-series, not all that much more expensive than our 4Runner but with a climate control system that really works!