Color selection expanded from only black, white, and silver in 1999 to include Dragon Green, Foxfire Red, and Proton Yellow in 2000-2001. The silver color tone also changed between those years, going from (I think, correct me if I'm wrong here guys) a lighter silver to a darker silver. For the interior Isuzu expanded from only red/black in 1999 to include gray/black options for 2000-2001. In my experience in searching AutoTrader, the red/black interior seems to hurt the resale value of 2000-2001 models vs. the gray/black scheme. This chart might make what I just wrote more clear:
So which year is better pretty much comes down to what color scheme you like and whether you want 16" (1999) or 18" (2000-2001) rims.