As for the ending, well how were they supposed to end it? The story had almost become ridiculous and it was already getting out of hand a bit, but for me it was ok. It's difficult to end things that have a cult following, or even put an end to it in general, just look what happened to the Matrix?
***SPOILER***
I'll tell you how they should have ended it:
First off, they shouldn't have killed off Naomi. Otacon getting hitched, Sunny getting a mom? That's a good ending.
Second, the number of times they nearly killed Raiden only to have him miraculously recover was rediculous.
After the initial encounter with Vamp in South America, he should have been out of commission until he showed up at the end to hold off the ninjas, with both arms, and he should have kicked their asses, not had his ass kicked.
Also, he should not have shown up to finish off Vamp during the second encounter with him, he had his chance, he failed, Snake did all the hard work, and taking that victory away from the player was asstastic.
ALSO, he should not have shown up to hold back this giant ass ship, to be "killed" once again. I already mentioned how rediculous him getting almost killed over and over was, but this was even more rediculous because there's no way he could have held that ship back. He was bracing himself against the very dock that the ship was moments before having no trouble plowing through!
No, what they should have done is have him almost be killed by Vamp, have Snake save his ass and then kill Vamp by himself, and then have Raiden show up only at the very end to allow Snake to complete his mission by kicking ninja ass like he SAID he would. Then he gets his happy ending with his wife and the kid.
Finally, Snake:
First Snake is going to die because he's prematurely aging. Then we find out that he'll have to kill himself long before that happens because the FoxDie virus has mutated. THEN we find out that he's got to sacrifice himself to a room full of microwaves to prevent the launch of a nuke.
Fer crissakes Hideo, PICK ONE!
Okay, in truth, I can live with all of those things. But what I can't live with is Snake miraculously surviving two out of the three, only for us to be left knowing that he'll die from premature aging a year or so after the credits roll.
Obviously having Snake survive the microwaves, the need to commit suicide, AND finding some miraculous injection that restored his youth would be just as rediculous as Raiden's multiple miraculous recoveries. And having Snake commit suicide would be a depressing end for a hero. Even more so than what we got with him presumably dying of old age a year after the game ends. But there was a way to end everything in a satisfactory manner.
After Raiden shows up to stop the Ninjas, have snake battle Liquid on the top deck. Rather than killing him though, Snake merely knocks him unconcious. Liquid does not reveal his real plan to Snake at this time.
Then Snake braves the room with the microwaves. You know, the one that was supposed to KILL HIM. And it nearly does, but he lives long enough to make it to the server room, where Ocelot uploads the virus.
Then, AS PROMISED, Snake DIES. Thus, he dies a hero, doesn't have to commit sucicide, doesn't have to die of old age, and there needs be no deus ex machina of Big Boss showing up and telling him that he was revived, only to have him be killed immediately by a virus which conveniently is overwriting the FoxDie virus that was going to kill everyone.
Then Ocelot still gets to cry about someone dying, only this time we see him yelling Snake Snake! instead of just hearing him, and we still get to end the game in the same graveyard where it began but this time with a big military funeral for a fallen hero who deserved it, where Meryl gets to pay her respects.
Oh and Liquid, on the deck, still alive? Well the ship blows up after the virus is uploaded, but not before he gets to have his final mologue explaining how this is what he meant to happen all along.
And Big Boss... Well, if he must, he could show up after the funeral, pay his respects, give HIS monologue explaining everything, and pull the plug on that old guy.
And then they can have that silly wedding, with Drebin, only in a proper church instead of on a stupid airstrip.
And that's how the game should have ended. Not with the crap we got.
***END SPOILER***