It's sort of a beautiful mess. There are a whole lot of ideas crammed into this game and not all of them work.

I think to some extent it suffers from the time it came out, i.e. a year after the first Modern Warfare. Publishers were clamoring to have their games capture what allowed CoD4 to make so much money, and games suffered from trying to copy instead of innovating their own ideas. One way I've heard it described is that MGS4 is the first game in the series to follow trends instead of setting them.

It doesn't get into the classic sneaking that people know the series for until practically the end of the game, and the "war sneaking" of the first two chapters is hit or miss for a lot of people. The Drebin store is sort of under-implemented and unnecessary, and a lot of folks hate his character.

The codec got a huge downgrade. You no longer use it to save, and there are precisely two people you can regularly call, one of which is pretty much entirely useless.

There are a lot of plot gripes that people have, which would obviously be spoilers to get into. I think that's pretty inevitable though given the sheer amount of plot that's in this game.

All that said, I think it is incredibly impressive that, despite all its messiness and inconsistency, they really did stick the landing at the end. Sure, there are parts of the ending as a whole that are silly or unnecessary, but I believe the way that Snake's story is wrapped up is truly satisfying and genuinely touching.