So I'm at 63%, saw the true ending, and just watched Episode 51. I have so many mixed emotions. On one hand this is without a doubt the best Metal Gear games as far as graphics and gameplay go. I am addicted to going back and doing the missions over, getting all the extras. It's gorgeous.
Even story wise there's a lot of cool things that this one did. Child soldiers, the parasites, language, even the metal gear fight was cool. But with all that being said watching episode 51 made my heart sink. I think the feud with Konami and Kojima hurt the production and we could have gotten and even more satisfying ending. I think when all of this was happening and a scheduled release date was on the horizon, Kojima had to make some unfortunate cuts, and for that I aim my disappointment in Konami and not him.
But thinking about there being two Boss's and Kojima's real point being there with you creating the face and the game overall wanting you to feel like Boss...is actually really cool. We've all went on a wild ride with Kojima over the years and Kojima is saying hey, you're Big Boss. You've played all these games and you've conquered the series. I think that is good enough for me. Would I have wished for that unfinished mission to be there and a little more coherence? Absolutely, but man, I got the feeling a lot of actually being Big Boss in this one and to be met with that ending solidified those feeling. It also like others have said can be used to explain MG1 and MG2.