Kojima doesn't really have anything left to tell with Metal Gear. He will finally be free to make other games, and I'm positive that the rest of Kojima Productions would follow him; they're his own personal MSF.
Konami really did lose something here. When was the last time something exceptional came from Konami that wasn't Metal Gear? PES is an annual sports game that gets consistently beaten by FIFA, Lords of Shadow 2 and Mirror of Fate weren't well received, Suikoden is dead, there was a new Contra teased a few years ago at E3 and we still don't have anything, Zone of the Enders HD flopped so 3 was canceled, Silent Hill was going nowhere until PT (which was created by Kojima, now will you look at that?) and I'm not even sure if they realize that they own Hudson Soft. Konami as a whole will be fine because of slot machines and things like that, but as a games company? It's not looking too great. They will probably make Rising 2 and remakes of the MSX Metal Gears before trying to outsource the series like they did with Silent Hill. They removed all likenesses that Kojima Productions had in MGS5, probably to distance him before they attempt to keep the series alive. Meanwhile Kojima will be in complete control over what he can make.
The thing that I want to know is when he leaves, does he get the rights to the Fox Engine? His studio was the one who created it since 2008, and he's always been the person showing it off, but was that on their own time or did Konami tell them to create it? I hope Kojima is the one who can use it, because it really is an impressive engine that would be wasted without an amazing game behind it.
I wish Kojima the best, and I hope that Konami learns to regret their decision.