Guys. The game has some major overly-far-fetched-plot-points that in the end are ALL related to the Big Boss revival, indicating that it was likely added much later in production. We know Kojima had an idea of having Snake and Otacon turn themselves in at the end because they are officially now as terrorists since MGS1, and be executed; a sort of "The Boss"-like ending where they would forever be remembered as madmen but who in reality saved the world. This also ties in to the trailer that was released months ago where you heard a guy speaking in the past tense about Snake, as if he was a legend or dead, saying that some believe he ruined the world, others believe he freed it. This ending was later changed, but the trailer wasn't release THAT long ago.
1- Eva doing her crazy act of throwing herself in the fire just to pretend she really thinks it is Big Boss' body.
2- Ocelot going through all he did in the past MGS games just to fool the Patriots into thinking he had become Liquid, and has such conceal his real intentions, but what's the point considering that his intentions were the same as Liquid anyway and considering that if The Patriots are aware enough to find out almost everything they would certainly find out he has been using drugs and self-hypnosis and what not just to impersonate Liquid.
3- It completely confused the part in MGS2 where Ocelot shoots missiles at everyone on Arsenal Gear and Fortune deflects them; at that point we should now pretend that Ocelot PRETENDED he turned off her device or something? Because if he didn't then it means Fortune really deflected the missiles, and if she had not everyone would have died there, S3 would have been aborted, Snake would be dead too. And then he pretends he's Liquid and runs away with Ray. Right.
4- The whole "Raiden went to Area 51, got his head chopped off, and became a cyborg ninja, thanks to the work of Dr. Madnar, the man who made a SNATCHER out of Big Boss by using his head and spine. That's right, it's really called "The Snatcher Project". Big Boss was a Snatcher?!?!
5- Big Boss being made from parts of Liquid and Solidus.
6- Dr. Madnar being mentioned in front of Snake and Snake having absolutely no reaction to the name. Feels like they had already recorded the scene when they decided to change the name to Madnar, and as such Snake's reaction remained as it was before the name change. That's a guess.
I could go on, but basically it screws up the whole series and the events of MGS4 themselves. If you actually play the game and never watch the Big Boss ending, everything makes sense (except for the corpse of Big Boss having his right eye, but that would have been easy to change late in production, same thing for the texture of the mechanical arm on Ocelot's, both are tied to the Big Boss revival arc). The story becomes almost TOO simple, when I finished the game I was like "oh, well I guess it turns out that this time there's no big surprise, they wrapped up everything without a crazy twist." And it's true, that's how the game really ends. But then the Big Boss ending throws everything upside down and complicates everything, making various aspects of the past games and even of MGS4 highly questionable, and quite unnecessary, unless:
When you take the above into consideration, it sounds to me like a few key but easily changeable aspects of the story were changed late in production to accommodate for the idea that a future Snatcher series will be set in the actual MGS world. Heck, Lucipher Alpha bight become the mutated FoxDie. We have Dr. Madnar, the Snatcher Project (with Big Boss being the first Snatcher no less), a candidate for Lucipher Alpha, all of this forced into MGS4' story awkwardly and to answer nothing in particular.
The lack of info on what the heck happened to Raiden, why Sunny is important at all, why it wasn't Snake who went to look for her as he said he would, etc., all sound like the bases to make a prequel too.
So my guess is:
MGS4 prequel(s) where you play as "human" Raiden and then possibly as Big Boss looking for Zero (that would be why they went through the trouble of making him come back to life 100% healthy).
And a new Snatcher series set in the MGS world. The game could have nothing to do with MGS but my guess is they'll have it set in the same world anyway.