On their site, Konami has said that it does take place after the events of MGS2. So its all good..
When I had first heard about MGS3 taking place in the 60's...I was like "what???? I wanna know who the patriots are!" But I ended up thinking it was the best Metl Gear game ever made.
Apparently MGS3: Subsistence is coming out soon (sorta like MGS2: Substance) with all sorts of cool stuff: online play (you playing against your friends) and I think there'd be a coop mode.
Plus you can play MGS and MGS2.
And other stuff.
