Personally, I'm glad they pulled the plug on this one. It kind of felt doomed from the start.
While the articles I've read about its possible "second chance" has been a little vague, the general feeling seems to be that Take Two was interested, but only if they got control of the Perfect Dark IP afterward. Microsoft obviously wasn't going to sign off on this, so the deal fell through.
(Personally, I don't feel the IP is all that valuable to begin with, but that's just my opinion...)
It reminds me of a story I read, from back when Microsoft bought Rare. When the deal went through, the boardroom at MS was ecstatic, as they thought they had just secured the rights to the Donkey Kong franchise, as well! WHOOPS!! But it goes to show how these decisions are sometimes made by people who are not as knowledgeable about the intellectual properties they're seeking to acquire, as they maybe should be.
Anyone who thought that Rare owned the Donkey Kong IP - at any point in time - really didn't bother to do their research