The project was formally announced at C2E2, but the story has been in the works long before that. Spidey writer, Dan Slott, revealed that he accidentally let slip a hint about Spider-Man 2099 way back in the "Big Time" story-arc and that fans may have noticed the hint missing when the trade hit stands.
I can tell you that somewhere during the "Big Time" era I screwed up and wrote something incorrectly that we later fixed in the trade. If you're an eagle-eyed fan of the "Big Time" era and you compare your comics to your trades, you'll be able to find my flub, which tipped my hand way too early that we were planning a 2099 story.
Slott also said the version of 2099 Spidey we see will be the original and not the Kirkman reboot and that the time traveling aspect of the story plays right into the current Marvel NOW! universe.
This time out, Spider-Man 2099 coming from the future will very much be like a character from one of the "Terminator" movies showing up. What he perceives to be good or bad is based on what effect it will have on the future, which means that stuff in the present that appears on the surface to be good might have terrible ramifications -- and vice versa.
If you're paying close attention to the Marvel Universe, there are a lot of time anomalies and time travel stories that all seem to be happening during Marvel NOW!. We have the younger selves of the original five X-Men now in the present, the "Age of Ultron," plus, there are a couple of other surprises on the horizon. And now there's this. Something seems to be happening to Time in the Marvel U., which makes it the perfect time for someone from the future to come to the present.
He also reminded everyone that even though this isn't the first time Spider-Man and 2099 Spidey have met up, it will be the first time for Dock Ock possessed, Superior Spider-Man. The rumor mill also suggests that this arc may be the return of Norman Osborn, but Slott has said only the story will featre "a" Osborn, offering nothing more.
Superior Spider-Man #17 hits stands September 4th.
Preview pages from IGN: