Metal Gear Solid 3 is the only title I take no issue with on any grounds.
I'm not a fan of the dated sneaking mechanics of MGS1.
I don't like the whole bit about Otacon's affair with his stepmother in MGS2 (that was just creepy).
I don't like MGS4's Tits n' Ass fixation (Big Mama's boobs and Old Snake's ass should never have been witnessed, and the B&B corps cutscenes feature more TNA than any other part of the game)
And I really don't approve of the sexualization of Paz in Peace Walker, especially the whole Date with Paz sub-mission, which I again found creepy.
MGS3 is amazing though, and is the absolutely perfect Metal Gear experience. If the HD version of 3 is ever released as a stand-alone on the PSN, I'll snag that faster than a pizza at a weight watcher's convention