MGS was phenomenal. It was mature, mostly non-cliched, and didn't have plot twists that were horribly absurd. Further it had this great message about potential and genetics. The twist at the end was genuinely interesting and not contrived.
I feel like the second one started off well, but halfway through just jumped the shark completely, and the series never really recovered after that. I admit, I only played a little of snake eater (just didn't like it I guess) and skipped other side-games, but I did play MGS4, and it went off the crazy train even faster than 2 did.