They discontinued the rear locker for the 2001+ models.
The 1999+ had a torsen center differential. Basically, the transfercase has a differential in it. This allows an AWD setting. A button on the dash locks the center differential creating a "normal" 4WD situation. The neat thing is you have 2WD, AWD (works on any surface), 4WD-Hi (only on low traction surfaces causes it binds like a "normal" 4WD), and 4WD-Lo.
99-2000 had the above and also offered a rear locker option. The best of all worlds.
Just have to correct one itty-bitty detail. On the 99-00 Limiteds, there isn't a button on the dash to lock the center diff. It's got a J-shift lever with a push-button 4WD button on it. Push the button, and you're in AWD (H4). Then, if you push the lever down (to H4L), your center diff is locked. Of course, you've got the L4, too. Some come with the option of that RR DIFF LOCK switch on the dash, that we've all come to love. And this is on the Limited models ONLY.
Just to point out the obvious, the center diff lock is NOT the same as a rear locker. Nothing too special, as both differentials are still open. Also, not sure if this was mentioned, but 5-speeds were discontinued from the 01 models on.
As for the best color of the 3rd Gen's --> Desert Dune.
EDIT: Hood scoop came on 99-00 Highlander package (basically Sport Edition) and 01-02 Sport Editions. They're just cosmetic and add nothing for performance. They look cool, though.