2000 was the last year for a manual transmission. 2001 was the first year for VSC, I wonder if that made a difference. My guess was, not enough people were buying the stick.
2001 was also the first year without crank up windows as standard equipment. I don't see many people complaining about not having crank up windows. Truth is, it was extremely rare to find a 4Runner in 2000 with either a manual tranny or roll up windows.