I couldn't make sense of MGS2's ending at all.
Partly because there's subtitles popping up but I don't who the strawberry float are talking. The ones that popped up during a black sequence.
There's a brilliant commentary on some of the final themes of the game here
. (I've linked to part two of that because that's where it gets really interesting, but part 1 is worth watching too if you've got the time).
Basically, one of the big twists was that the Patriots were revealed to have been orchestrating the entire Big Shell incident to fine tune their creation of the ultimate soldier. The revelation that the AI are behind everything, and that they are actually looking out for humans best interests (see part 1 of the vid), is probably the biggest twist in MGS (probably - I've still not played 4 )
. All that said though I can see how 3 clinches it for most people - it is cinematic beauty and really tugs at the heart strings
The subtitles at the very end you refer to, IIRC, do say something confusing that doesn't seem to make sense at first. Something like the Patriots have all been dead for hundred of years