Since finishing the game, I've taken a lot of time and turned the whole story and ending over and over in my head several times, looked at it from all the angles that other posters have presented, and I still think it's inferior to MGS3. Different people have provided some great justifications as to why/how they feel it was very satisfying or even perfect, and I definitely respect that. But for me I'm still just dissatisfied with how things were handled.
I know it's been said a million times, but I really was expecting Kojima to make us pull the trigger on Snake, and toward the end like others I thought it would end up being a noble thing to do, since he would soon become a walking doomsday device. He would finally give every last bit of his life protecting mankind, and it would be extremely concrete since we would know for sure how and when he died. This game instead went with a happier ending, which is OK for some, but I was really expecting the suicide scene. People mention that it's a cliche, but how many other games have done that? Particularly really popular series' like MGS? Apparently it's a trend in anime, but I don't watch anime so to me it was a pretty original concept for a game. For me personally, much of the impact was lost because of this. I like surprises, so I like the twist on the credits with the pause on Big Boss' voice actor, Kojima got me on that one for sure. It was still strange to see him there, but I can appreciate the final resolution that scene provided, even if I preferred Snake's suicide.
(Side note-as for the gunshot we hear, is it possible that it came from the Patriot Big Boss was carrying? Maybe he saw Snake about to kill himself and shot it in the air, and Snake removed the gun from his mouth and fell down sweating, panting, before he realized exactly what happened. The only other possible explanation is that he accidentally shot it after he took it out of his mouth, or maybe he jerked it out of his mouth and shot it elsewhere in one final attempt to keep himself from pulling the trigger on himself, and was still reacting from the emotional impact.)
My first moment of story disappointment came at the very beginning of Act 2, when Snake is crawling through the brush while his conversation with Campbell plays, where he says that the twelve founders of the Patriots bit was "a load of crap." That was a big red flag for me, that they would take something so mysterious and something that was apparently a huge piece of backstory (in fans' eyes, anyway) and play it off as just false information.
Perhaps that was the intention all along, but that just seemed lazy. I'm somewhat satisfied with Vamp's explanation, but I have to wonder that if they had nanomachines capable of such healing, why weren't they more widespread? That's a tiny issue admittedly, but something I thought of right away.
I also think the Liquid Ocelot facet in this game is a double-edged sword at best. Someone else here (I forget who or I'd give credit) worded it well explaining how Ocelot ended up being very similar to the Boss, in that he gave his life for the mission, which of course in this game was to end the Patriots' reign. (Fitting since he's her son). I think that is pretty brilliant now that I look back on it. On the flipside, though, I really was expecting what was seemingly happening, a true complete possession by Liquid. It felt like a "just kidding, lol" moment when I learned the truth at the end. I also think the game could have used one more boss fight at the end, something truly massive in scale. The fight with Liquid Ocelot on top of Haven was a nice parallel to the Rex fight in MGS1, but I was expecting something else to happen afterwards.
I think Act 3 is a really creative take on the stealth gameplay, and a fantastic throwback to one of MGS3's more memorable stages with the motorcycle ride, but the more I think about it the more I get the feeling that fanservice was too much of an influence in this game for it's own good. I love seeing nods to other games in a series, whether overt or subtle, and I know that Kojima had to include such characters and scenes as a means of tying up loose story ends, but it's just such a contrast to MGS3, where we got so many new faces.
Anyway, that was too long and I appreciate anybody who actually read all the way through it. As far as the overall story and game development went, I was reading Ether_Snake's thread over at TUS (I won't link to it since he's currently banned here) and I think he's on to something with it, despite the conspiracy theory accusations he got in a few of the replies. I can't say every bit of it is probably true, but like him I have a feeling that the overall story and scenario of this game underwent some massive changes during development, for the worse. I think the original concept was probably significantly more complex.
I would love to see an alternate ending or two in the eventual Director's Cut of this game.
