I made the move from a D200 to a D2x and part of the reason was better auto focus. Its not a night and day difference but focus is definately quicker to aquire on low contrast scenes with the D2x. Plus you get 9 cross type sensors as apposed to the 1 cross type on the D200.
When manually focusing there is also a little arrow either side of the 'in focus circle' in the viewfinder to guide you with fine tunning manually.
If you don't mind the extra cost, size and weight I'd go with the D2x every time, its not just the focus thats better, its just an all round work of art! (oh and the D200 is actually bulkier than the D2x when you have the grip on it!)
I now have a D2h and a D2x. I was looking for another body to compliment my D2h and I looked at D200s. IMO, unlike the above post, the AF is much faster on the D2h and D2x than it is on the D200. I shoot dog agility and the dogs are moving very fast and making eratic moves and quick changes in direction. If you are planning on shooting sports or other fast moving subjects, by all means get a D2x. The Cam2000 AF system in the D2h/D2x is hard to beat.
Another thing to consider is battery life. The D200s are known to go through batteries pretty quick and I can shoot almost all day (1200+ pictures) on a single battery.
I still say (for me) the difference wasn't that big, not with birds in flight at least. As long as I keep the bird in my sites they both tracked just fine, if its something erratic thats all over the viewfinder even the D2x can have troubles.
Low light and indoors is where it shines though as it continues to be accurate and not hunt anywhere near as much as the D200 in those situations.
Battery is sooooooo much better though! One D2x battery (and I have the lower capacity ones!) out shoots two D200 ones!