Jumping the Shark. When you realize all the mysteries need answers, but you never actually thought it through.
Metal Gear Solid IV is meant to be the concluding chapter in the Metal Gear series that ties up all lose ends and has gamers crying when it ends while utilizing the most polished MGS gameplay. In many ways, MGSIV fulfills everything I've mentioned. The game does conclude the story and the gameplay is polished to a brilliant shine.
MGS4 basically has a story that is stuffed with filler, cheesy moments, and plenty of pointless fanboy jerk offs. A good analogy is Star Wars Episode 1 Guido and Anakin scene as well as C3PO. Neither C3PO or Guido were really necessary in Episode 1, but they were included to get cheap reactions from fans. Well a lot of equivalently lame scenes happen in MGSIV just for the sake of telling the audience "oh hey remember that one reference from the previous game?"
MGS4's largest story flaw is that it's clear they never had answers for the mysteries they came up with. Practically everything in the game was explained with nanomachines or just pure coincidence. Worst of all, Naomi Hunter's character hijacked way too many scenes, which only made Snake's goals even more pointless.
In terms of gameplay, the game is perfect with the exception that there isn't enough areas in the game to fully utilize everything available to you and you basically have to gimp yourself if you want to make the game challenging or play it stealthy. MGS4 practically deviates away from the Stealth gameplay and rewards you for going the action rambo route every time. This may be okay for some, but when I play MGS, I play it for its stealth gameplay.
In conclusion, Metal Gear Solid 4 is a big disappointment in comparison to the perfection that is the rest of the series. Perhaps if the game had an editor to cut down all the pointless scenes in the story, more levels to utilize all the gameplay introduced, and reduced the availability of weapons to keep the stealth gamaplay intact, MGS4 would be drastically better.