You pretty much summed it up. A/C is standard on any VehiCross... what changed from 99 to 00-01 was that Isuzu added a more sophisticated climate control system. Look in the gallery for some dash pics and you'll see the difference.
99's have 16-inch wheels, 00-01's get 18-inch wheels. The 18's have been known to pit and peel.
I believe 00-01 models may have a lengthened strap for when you fold the rear seats down.
Other than that, well... 99's came in astral silver, ebony black, and victory white. 00-01 added proton yellow, a darker kaiser silver, foxfire red, and dragon green mica. Different exterior colors come with different interior color options. With some you only get red/black, others grey/black, and some get a choice between the two.
Pretty much the only added options for any of the years were a roof rack and Ironman graphics package (victory white only). Everything else is standard, and you get some pretty cool standard equipment.
Oh, I saw somewhere that the 00-01 or maybe just 01 models switched over to Sony Xplod speakers too, but not real sure on that one.