Okay Yahtzee, I get that some, including you may have a problem with Kojima's storytelling, but he didn't make the story this time around! Sure you can say that he didn't know about the iffy development process but when you start up the game it says "DEVELOPED BY PLATINUM GAMES"!!! I was wondering if this would happen, I would've loved to hear him comment on Platinum Games making the game.
Although I do agree with many others that the end was very over the top, but honestly since the main villain was pretty much introduced then and there (yeah you saw him a bit earlier but still) so they had to make him memorable somehow. I won't remember MGR for being particularly smart or anything like that, but I will sure as hell remember it, final boss Dragonball Z-style, fun, just what this spin-off needed, eh?