An interesting bit from another interview with Kojima that was conducted when he was in Dubai, from DvLZGame (keep in mind this is a translation).
Kojima was asked if Ground Zeroes will be released for next gen systems. He answered that this was ‘a secret he could not talk about’.
The interviewer continued by saying he expected Microsoft and Sony to announce their new consoles this E3 or sooner, and he expects to see more of Ground Zeroes then, since he believes it will be for those systems. Kojima replied by saying: “We will see about this one day… Maybe sooner than you think.”
Of course Kojima is deliberately being vague here, so how to interpret his comments is hard to say. But it does seem to at least imply the game is going to be available on the next generation systems. At the vey least Kojima is working on next gen consoles with the FOX Engine. All we can do now is wait.