Well I'll add my notes as I think of them and link the articles that I've found over the last year...
*When they released Call Of Prypiat they were already busy with the new s.t.a.l.k.e.r 2 engine.
*There will be females in the game.
*New mutants (not confirmed)
*There won't be that many weapons but they are improving the whole weapon upgrade system.
*Greater emphasis on survival in the sequel
*New areas - triangle of CNPP, the cities of Chernobyl and Chernobyl 2 (Durg-a-3 or the infamous woodpecker antenna, who knows the story behind this?)
*There will be a import-a-weapon feature.
*S.T.A.L.K.E.R. 2 will support DX11
*Xbox 360 won't be able to handle the game, apparently the Xenos GPU is just too dated for such a intensive engine. (Unconfirmed)
*Apparently finding weapons and ammo in the new game will be a lot harder (again not confirmed)
*I feel like I'm making all this up, but I swear I'm not... I just enjoy going on forums.
*GSC is considering adding DLC's to the game after release
That's about all I can think of now, but here's some other VERY interesting s.t.a.l.k.e.r links for you guys:
http://www.moddb.com/games/stalker-build-1935
http://www.moddb.com/games/stalker-oblivion-lost
It's Monday morning so my brain is extra slow and tired after watching too much top gear last night.