Some more things:
-I do kinda feel that MGS is surprisingly Metroidvania-esque, in that finding items and unlocking previously closed rooms is a key part of the gameplay (perhaps as important as the stealth itself).
-Just to ask, do you guys know any major examples of a "man vs. aircraft" boss battle in any game released before Metal Gear Solid? I know that it's become quite popular considering how Grand Theft Auto III, Half-Life 2, and Uncharted 2 all feature "man vs. copter" boss battles (note: I've never actually played any of those games, just heard that they have helicopter boss battles. Also I've watched an LP of Half-Life 2 before).
-The last two bosses requiring use of one item (sniper rifle for Sniper Wolf, AA gun for Liquid Snake's chopper) only during the fight kinda reminds me of dungeon bosses in Zelda games, although obviously here we were getting the aforementioned items in order to fight the aforementioned bosses!
-I've heard that there is a boss battle against a jet fighter in Sons of Liberty. Looking forward to that!
-IMO Metal Gear Solid's gameplay and level design are just as "ambitious" and "groundbreaking" as its story.