I think this can only be said to a marginally greater extent than what people were saying about Metal Gear Solid 2 after it was released. Alot of people said the exact same thing. Then Kojima turned around and gave us arguably the best game in the series.
The long cutscenes and convoluted plot was a tribute to his own style; it was almost a commentary on Metal Gear and Koji Pro itself. That being said, I don't think anything done in Metal Gear Solid 4 sabotages the likelihood of an effective sequel.
He said himself in a Game Trailers interview that he's not the kind of developer who revisits his older titles, but he would be open to the idea of exporting it, similar to what Silicon Knights did with MGS1 on GC.Originally Posted by Fonz