I think Skaw hit the nail on the head, even if this is Snake's last mission, and the torch is passed onto Raiden, I could easily imagine them coming up with remakes of the old Metal Gear and Metal Gear 2 again (the ones that came packaged with Snake Eater LE). Plus you could always throw Snake into some other side-missions, what was the time gap between Metal Gear 2 & Metal Gear Solid?
I just hope they get rid of Snake's mustache, can't stand that thing. And if Snake goes down, I'm hoping Liquid/Ocelot going down also finally, none of that "I LIVE ON INSIDE MY ARM!" bullshit.