Setting aside the themes of alienation and purpose that run through most of his games (because that is a can of worms) it’s hard not to say that Kojima's work, at least in the modern gaming era (call it PS1 and later), definitely put into practice some pretty wild stuff I'd certainly consider unorthodox and radical--it's worth juxtaposing the cinematic/filmic presentation and direction of Metal Gear Solid with your CO telling you, in-universe and in-character, to "Press the Action Button to..." while in the next sentence somebody else is going on about the “physical” limitations of your radar system. That didn’t happen then, it doesn’t really happen today, and when it does it’s clearly an homage to that sort of blurred-lines unorthodoxy that MGS, whole not creating, certainly made A Thing for a lot of people.
Metal Gear Solid 2 probably counts for a lot, IMO. To an extent it might have some "Seinfeld is unfunny" to it today, but when it came out there was just nothing like it as a downright subversive story and experience. Still kind of isn’t.
That isn’t, of course, to take away from the games you mention, because those are all great games. But Kojima’s stuff fits that description for quite a few reasons, too.
(Agreed that Minecraft doesn’t belong, though, and I am very familiar with it. ;) )