MGS1 was great because of Mei Ling. Ohhh, she taught me so much. And the bosses were cool. Vulcan Raven, Psycho Mantis, Ocelot (I loved this one), and the fist fight with Liquid Snake is great. I also thought the wolf scene was genius.

MGS2 was ok, Raiden was a pretty cool character. Just because Snake isn't there for all those fan-boys out there, doesn't make it a good game. I'm actually glad Raiden will be back. MGS2 must have had the craziest and most confusing storyline.

MGS3 was on the whole the greatest of the series. The stealth missions and actually finding your own food was great. You actually had to heal yourself and remove your bullets to survive. You needed to eat. Unlike the other two where all you had to do is have a ration, this one went all out in order to bring that feeling of reality.

EDIT: And the fact that in the other 2 games, if you were being chased by enemies, all you have to do is run out of the room. However, there isn't s cheap trick like that in MGS3. Stealth % instead.