I too am a huge MGS fan ever since MGS on the PS1. I do feel he has over egged the story a bit now, and the cut scenes can start to grate, but long cutscenes and complex story arcs are a trademark of the series, and you don't buy a MGS game if you don't like them. Who's to say they didn't know where the story was going to end anyways, and were just waiting to get to this point, as this is supposedly the final game. Or did they just make it up as they go along.
For me MGS's always been more about the cool stuff you can do, and the fantastic set-pieces than the story telling, though I've always thought the story was better than some drivel that's released.