I'm still not sure how anyone can determine which MGS game has the least reprehensible story, though I suppose the first one was decent enough until Liquid shows up and starts ranting on about genetics. 2,3, and 4 though.....oh brother. I just gotta shake my head in disbelief at the people that honestly and truly enjoy this. It's one big pile of steaming nonsense wrapped up in a very pretty package....like Mormonism. MGS is the Joseph Smith of videogames.
I rank 1 the worst because the whole I Killed A Boss, Now I Get To Hear His Life Story thing is terrible. And the ending with Naomi or whatever ranting about living life for 20 minutes is unbelievably sappy. And then you get to hear a sappy song with moany vocals that MGS fans worship.
The transgressions in 2 really don't bug me that much. The whole ordeal strikes a delicate balance between ridiculous and awesome. Some of the Rose stuff was a bit too much, but Otacon fucking his mom--pure awesome. And the late game narrative shift into wacky AI mind fuckery probably makes me forget a lot of sins.
The 3rd game is just really solid, all around. It doesn't hit the heights of 2 (for me), but there's really not a low in it. I'd say it's the most consistent game in the series. If I were doing a fair ranking, I'd probably rank it right alongside 2 as my favorite.
You see, I'd say 2 is my favorite because of how memorable it was when playing it the first time. The virginal playthrough counts a lot for me. MGS3 is more replayable, but it never had the impact that the first playthrough of MGS2 had for me. MGS2 was like, "woah, videogames can have stories that do interesting things," and while MGS3 was good all around, it didn't stick the shocker in my ass.