I loved the first two but am a bit nonchalant about Snake Eater. I beat the game, I think the ending is fucking amazing (The Boss and the Vulgin), but I just don't share the view that the game as a whole was really that good. I think I would've liked the jungle setting if it were truly wide open, but to me, it felt just like being inside a building with trees growing up and whatnot. Going from one area of the jungle to another didn't seem to have any type of coherency to me; like I said, it felt like I was going from one room of a building to another.
I understood the storyline of Snake Eater far more, and that's a good thing. But when I played against the bosses in this game, it felt disorganized. Like, "Here's a boss. Fight it!" That probably wouldn't have been a bad thing, except they tried to piece them together via a storyline, and I just felt that it didn't fit together very well.
I also think the food system is WORTHLESS and just a fucking annoyance, and I don't like the backpack idea. I wanted to just have all my items already equipped. I absolutely hate going into the menu, but I found myself there quite a bit.
CQC was a great addition, though, even if it was more just for fun than an integral part of the game.