MGS1 was a great game that had a very strong story. It had lots of plot twists, sure, but I don't think it had quite reached the level of craziness that later games in the series would exhibit.
MGS2 was confusing as hell the first time I played it, and I admittedly didn't care much for it. But after I played it a few more times and read some of the extensive analyses that can be found online, I actually learned a lot of important concepts (meme theory, post-modernism, etc) that I never thought a videogame would teach me. Not my favorite in the saga, but I have a lot of appreciation for what it was trying to do.
MGS3 is my favorite in the saga. It wasn't as convoluted as MGS2, due to the fact it was a prequel. I feel like the game lost a lot of the philosophical verve of MGS2, but the fact that it focused more on emotionally involving storytelling made me enjoy it more. Still one of the greatest games ever made!
MGS4 I think actually made things much more convoluted instead of explaining them away nicely. I also feel like it ultimately weakened a lot of the ground that had been covered in previous games all in the name of fanservice. I'd call it the weakest game in the saga.
So in conclusion: MGS has one of the most incredible stories in gaming, but it doesn't end satisfactorily.