Metal Gear Solid: Portable Ops.

I think it's faaar superior to the sequel in just about every aspect, but within the Metal Gear fandom it tends to be crapped on a lot in favor of Peace Walker. That being said, the MG fan base tend to be very fickle and worship Hideo Kojima as if he were incapable of putting out a bad game (hint: he has put out many lackluster games), and seeing how Portable Ops wasn't a Kojima game it gets pushed aside as "non-canon" despite the story having an impact on every game released after it. But this is the same group of fans who absolutely hated MGS2 for the first few years it was out but now clamor about what a masterpiece it is, so I'm not surprised. I could go on a multi paragraph rant about why I think Portable Ops is the superior game, but I'll save that for a YouTube video in the future. It is truly the hidden gem of the franchise and was a major influence on the titles that followed it.

Also, as an extra jab to Kojima: the best/most influential game he's put out in the past decade was a demo for a game that never even came out: PT. MGSV had the ability to be a masterpiece but he was too busy making business deals to milk the franchise in every possible way with crossovers and merchandise that the game we ended up getting was barren and unfinished. Fun, but unfinished.