He is easily one of the greatest game developers of all time. His games have gameplay ideas others don't even dream of coming up with. He is a master of game design, a master of how gameplay mechanics should interact with a world, a master of creating exciting action moments, a master of developing intricate gameplay systems and the creator of many of the greatest boss battles of all time.
Every MGS game was an evolution, so many franchises get hung up on doing one thing over and over, his games were always truly unique and in many ways groundbreaking. MG2 and MGS has interactions that just make sense and work as they should but so many games never think to get right. Foot prints in the snow, having elements of the game needing you to find something in the real world, the use of every feature on a console and controller to create memorable moments.
His games have surprises on top of surprises. In MGS3 the amount of hidden systems puts to shame other games. You can use the radio to heal or call an air strike. You can overheat guards talking about weapons caches and blow up that cache and later in the game enemies now have worse weapons because you did so. Bosses have so many unique ways to approach them.
He is a master of gameplay pacing, constantly throwing new mechanics and situations at the player. MGS4 playing one way for half a game then going off on a huge curveball (I know some didn't like it but I loved it), no you are in an epic bike chase that you play, epic metal gear battle that you play, mashing the controller to stay alive; he keeps the player playing the most memorable moments in the story. The final 3 hours of MGS3 are the greatest final hours of any game in history, it's still not topped because of how many varied situations are stacked one on top of another with the story hitting the climax in perfect harmony.
Then we have MGSV which is unfinished, has many problems but the gameplay is unmatched. It controls like a dream, it has options galore and even though it's a lot more spaced out it still has those surprising moments.
His games have a certain quality to them that is a signature, you can tell it's a kojima game, very few game directors have that. His track record is nearly perfect, each MGS game is a masterpiece in its own way.