I think that I'm going to sound like a complete Asshole, but Metal Gear Solid 4: Guns The Patriots. I played the game first time, and I thought it was the best game I ever played. But then again, I am a huge fan of the series, so my opinion was bias. So I managed to shake off the fanboy in me, and I played through it again, making sure that I could not think back to the previous games. The storyline in a game is really important to me, because no matter how much fun I'm having, if there is no backbone to it, I will find it steadily less interesting. The Metal Gear series was well-known for having amazing storylines, and as I played through the series I would be prepared to back that up. Guns of the Patriots did not break the tradition of having an brilliant storyline; in fact, I don't think that the storyline could have been improved. What I was annoyed about was the execution; this is why some people didn't like MGS2's storyline. While it was very well written, it WASN'T very well executed. MGS4 is the same to me.
For me, while the Codec wasn't a massive ladnmark in gaming, I loved being able to talk to support characters about where to go next, or how a certain gun was. I was hoping to be able to use it in real-time, that would have been a dream come true. But Hideo destroyed the Codec by limiting the use to 2 characters, one of them I never felt the need to speak to ever. I never found Metal Gear Solid 4 bad, it's just that at the end of Act 3 I knew that the execution of the storyline was not only confusing, (even to me for the first playthrough) but it could have been a lot better to follow had it been explained differently. As I said, nothing wrong with the story, just the execution.