personally, i like ATI, but for the money - go with Nvidia. As stated already, the 6600GT is more bang for the buck than the ATI 9800xt.
As for the Atlantis thing, i would guess that the Atlantis is probably just some sort of marketing name. it's probably a 9800 pro with a different name.
The difference between the pro and XT versions - obviously 128meg of memory. but you wont see a dramatic improvement in any games.
Bottom line: Go with Nvidia 6600GT now or wait a couple of months and go with the 6800GT when the new cards come out.