The MGS series is a love or hate thing. A lot of people love it, a lot of people hate it. I, personally, love the series.
The first one I played was MGS3, to start chronilogically. I immensily enjoyed it. The storyline was interesting, the characters were awesome (especally the Boss), and it was fun and atmospheric sneaking around the jungles. I didn't enjoy the boss fights as much (with the exception of The End, which is my favorite boss fight from any game), but all in all I liked the game.
Unfortunately, MGS3 spoiled me with it's 3rd person camera, so when I played MGS1 Twin Snakes I had trouble adjusting to the top-down view. MGS1 is probably my least favorite in the series, because the characters didn't interest me as much, and Shadow Moses wasn't as fun to sneak around in as the jungles of Russia. I did, however, love the boss battle against Psycho Mantis, and the Ocelot torture sequence gave me goosebumps.
MGS2, I liked alot. I didn't mind the switch to Raiden, though he didn't really interest me all that much. But it's my favorite plot/story in the series. I didn't find it confusing at all, though maybe that's because I had previously watched and fully comprehended End of Evangelion, so I was better prepared. The Big Shell was fun to explore, especially the areas outside.
MGS4 is the love it or hate it game for me. I loved the advanced stealth gameplay, I enjoyed the variety of environments, and I even didn't mind the cutscenes, since I'm a patient gamer. The boss battles were also some of the best in the series. Unfortunately, some of the best action sequences in the game were non-interactive, regulated to cutscenes instead, and when you switched over to gameplay some of the encounters were underwhelming as a result. I also didn't like the soundtrack as much.
So, I guess I would say I love the series more than it gets on my nerves.