If I can recall correctly, didn't Kojima give the same spiel about MGS 3 being his "last game" in the series?
He doesn't think far ahead beyond the game that he's currently releasing for a time. It's this lack of foresight, that's the cause why the canon is such an incoherent mess.
Honestly reading a lot of interviews, I think the main reason he keeps saying that is because he keeps getting tired of being essentially forced into making new stories for Solid Snake. Realize that after MGS2, people wanted more of Snake with Raiden taking over in the Plant chapter (nothing against Raiden at all, I like the character after all). He said that MGS3 was actually a huge sigh of relief for the team since they were already familiar with the PS2's engine, and it was something that the crew really had fun with when making it. I can't imagine finishing a game like that only for people to want the next thing afterwards because they wanted more Solid Snake.
It's also why his interest towards Snake probably slowly waded over time, favoring Big Boss in many other titles directly after MGS4. Not that I'm dissing Snake though, I LOVE the guy, but while Kojima's choice of words were poor, I interpreted it more as him finding more leeway in characterizing Big Boss' tragic/tortured aspects as a fallen character compared to the more stoic and awesome deadpan snarker that was Snake. I guess it's why he even inverted that in MGS4, it sort of glorifies the "old" action hero days while deconstructing it by actually showing how badly it's taking a toll on Snake as a whole (as much as people hated it, I really loved the whole idea of "Old Snake" and it really allowed me to sympathize with the character even with the mess that MGS4 was).
Well to add more fun to the Para-Medic/Gray Fox talks, here's a little something I found hilariously ironic in light of her fate:
"Snake, did I ever tell you the reason I got into science in the first place?
[No, I don't think you've mentioned it before.]
Well, when I was a kid, back before I could go and see any film I wanted, my mother would read books to me and my sister to pass the time. Eventually, she read us one book about a scientist trying to create, and control life.
For a while, it was my favourite book. I remember reading it over and over again, and even thinking about what I would do if I were in the scientists' place. It must sound silly to you, but it kept me interested in the sciences while my sister and my friends grew into the normal interests teenaged girls had.
When I heard that they were finally releasing a movie based on the book, I could hardly contain myself! My parents didn't want me to see Frankenstein, because they said it would scare me, but I snuck out the night it was released and saw it three times in a row. My parents were so worried because I was gone for so long, that when I came home they weren't even upset that I had left in the first place.
Snake, Frankenstein dedicated his life to try and better humanity, and he paid for it by being destroyed by his creation. It's an amazing thought that shows not to obsess over something too much, or it will ruin you. Remember to keep a level head in the battlefield.
Imagine..being destroyed by your own creation. Good thing it was just a movie, huh?"
You gotta love the irony, especially in retrospect.