#8: Portable Ops. Absolutely insipid plot, not letting the Boss rest as a story element, and pretty boring game design.
#7: Peace Walker. Basically the above, with a slightly less insipid story. Base building mechanic was cool though.
#6: MGS4. There's a lot in MGS4 that's done well, but it's undermined by some unforgivably long cutscenes and some really bland gameplay sections.
#5: Ground Zeroes. More of a demo than anything, I suppose, but the gameplay is by far the series' best. Price tag's a bit of a sticking point. Buy digital for last gen and it's all right.
#4: MGS1: A very good game at its time of release that has aged pretty poorly.
#3: MGS2: A very good game at its time of release that has aged pretty poorly, but also has some cool sub themes explored in the background.
#2: Revengeance: Possibly the only Metal Gear game that hasn't let its story get in the way of its gameplay. Rising is fun, intense, and incredibly silly. Wish it would allow for on the fly weapon switching, though.
#1: MGS3: Arguably one of the best endings of all time. I do wish someone would remake it and fix a few of my quibbles, such as having to pause the game to change camo/heal yourself, but meh. As it stands, it's the only game I can look to in the series that's managed to keep a fairly serious story together well while still mostly holding up to this day in the gameplay department.