J.J. Abrams Tells All

In this interview, and not just about Mission Impossible: III, but about Alias, too. He even answers the question of why Milo Rimbaldi basically disappeared from the series after the second season:

Q: Will Milo Rambaldi play a significant role in the “Alias” finale, or has that ship sailed?

A: There will be a Rambaldi component to it. We would have actually gone there far more — and in greater detail, as we originally conceived it — if the network had been more amenable to that. But they were always very anti-Rambaldi, so we kind of had to pull back.

Q: Did you ever consider a circumstance that would have necessitated casting Rambaldi?

A: We actually have. In a flashback once, you actually saw a piece of his hand, but you never actually saw who he was.

[brief pause] We actually have — yes.