Probably still MGS3: Subsistence.
Snake Eater was broken to me with the locked camera angles; it essentially required level memorization and patterns, which was a no-no in game design to me by the 6th generation of hardware. Given that Snake Eater has not been republished/re-released post Subsistence seems to be an acknowledgement of that opinion.
But story, pacing, impact, character development, Metal Gear universe development, etc. were all on the mark.







