My problem with the series is each game, aside from the first one (which is by far my favorite...) has a big flaw:
MGS2 - too many Codec scenes, Raiden... LOVED the plot though
MGS3 - annoying injury recovery system...
MGS4 - game falls apart after chapter 2 (though I liked chapter 4 quite a bit!), some annoying camera stuff, main plot twist was a bit disappointing
I'd say overall I'm a big fan of the series though...