Wait, what do you mean? Big Boss shows up in MGS4? No he doesn't, Snake shoots himself in the graveyard and then it all ends! Right??? Yeah, yeah, that's what happened, yeah, definitely.
...Goddamnit MGS4 you suck so much.
It's the best ending in any video game ever, and you're just crazy.
MGS4 wouldn't be half as good without that ending.
That ending was the most insane thing I've ever witnessed in a video game. That's saying some, even by MGS standards. Without that ending MGS4 wouldn't be half as good as it was. That last 40 minutes (seriously, 40 minutes AFTER the credits roll. How dumb is that?!) was incredible.
But on to the the topic - I'm pretty sure Kojima said in an interview last year that he is "willing to break canon to be able to tell the story he wants to tell" or something like that, so who the hell knows? I'm sure they'll come up with some crazy (bullshit) reason to explain it all anyway.
I enjoyed the ending to MGS 3 much more, MGS4 was crazy, but I didn't enjoy it nearly as much as the EVA reveal, and the revelation about The Boss. Tears wanted to stream, I didn't let them.
@the_ruiner: But none of the Metal Gear games, have good game play. Serviceable sure, but not good. The only reason anybody talks about the franchise, is because of its ridiculous story. If he doesn't care about the continuity, then the whole series is irrelevant.
My favourite story in MGS is MGS 3, and it's not the Cobra Unit that stuck with me, no. It was the cold war story, the relationship between Big Boss and The Boss, the twists and turns of EVA and Ocelot and the story behind the creation of Metal Gear. I also LOVE the MGS gameplay. I really enjoyed the hunting systems, the stealth mechanics and the boss fights. Dude even the little cutscenes you get when you're digging out bullets and pouring ointment on your burns.
Just because you can't adapt your play style to fight the MGS series, doesn't automatically mean the gameplay is bad.