As a kid, MGS2 was my favorite. In college, MG: AC!D, and now as an adult, MGS:V.
I think that Kojima has gotten less absurd, but more pretentious, and I'm fine with that; it's hard to appreciate video games much otherwise.
My favorite boss fights are: Vulcan Raven in MGS1, Fat Man and Metal Gear Ray in MGS 2, and The End in MGS3.