I borrowed GOTP off a mate, and gave up when I got to boarding the sub so I've no idea what happened next - although given Snake was pretty much on death's door by that point anyway I think it makes sense that he's finally been retired. They were dragging it out no end.
I'm surprised they kept the MGS name, though - I'd have thought a Raiden-focused game would be worth a rebranding/spin-off. Looking at that trailer, it's a totally different format now. Raiden was never "Mr Stealth" like Snake, as proven by all the hacking of limbs and chopping down of buildings.