The Microsoft press conference debuted quite a few games, but it had a distinct lack of Crackdown. That doesn't mean the franchise is dead, though, as Microsoft Studios general manager Phil Spencer says he'd like to see it return when the stars align properly.
That's not exactly a promise of a new Crackdown title, but it's something. At Microsoft's initial Xbox One presentation, the company showed off the user interface, which had a subtle appearance of an Agility Orb. Later, a (largely debunked) rumor had Crackdown 3 on Microsoft's show list, along with other games that didn't appear like Banjo Kazooie 4 and Fable 4. In the days before E3, though, this combination of factors had some fans excited for a Crackdown announcement that didn't come.
Whatever team Spencer might have in mind, Crackdown 2's Ruffian Games definitely isn't on the project. It's currently working on its self-funded Tribal Towers, along with a "top secret project" that it specified is not Crackdown 3.