So I just finished this game a couple weeks ago and wanted to chime in with my thoughts on the game.
To the point, I was extremely dissappointed. This is easily my least favorite of the four. As with MGS2, it seemed that the ridiculous story could not get out of the gameplays way. What really annoyed me with this story was how each ridiculous twist was rationalized with some half-baked sci-fi mumbo jumbo. With a good twist, the viewer needs to be set up so that it fits retroactively. Kojima apparently doesn't know this. Which basically means that you can never rely on anybody to stay dead or any plot development to have permanence, which then takes all emotional meaning from them.
As for the gameplay, I didn't like how there is such a great arsenal of weapons available to us from the get-go. In MGS1, you often needed to get a new weapon or device in order to proceed further. This made each weapon/device unique and important. In MGS4, they just throw weapons at you like crazy and none of them are absolutely vital to your progression (besides that nanomachine supressor). Also, after my first play through, I have tried to play while skipping the cutscenes and I'm amazed at how little gameplay I have found.
To me, MGS4 perfectly embodies the wrong direction in which videogames should go.