What if Frank Black had become Scully's new partner instead of Doggett?
The timing would have worked out perfectly. In the middle of season 6 of the X-Files (which was the middle of Season 3 of Millennium), the "Rebel Aliens" basically wiped out the entirety of the Syndicate that the main aliens trusted to make way for the coming alien invasion. It would have been fantastic if the aliens then moved to the Millennium Group to take over the Syndicate's work, which would also fulfill their prophecy of the end times, and they would have total control over how everything ends. We know from the final X-Files episode the end time to be December 22, 2012 (not necessarily the end of the millennium, but no one said it had to be that precise).
It also would have been utterly amazing if once Mulder went into hiding, Scully partnered up with Frank Black for the 8th season, completely merging the 2 shows together in order to fight the coming apocalypse (while solving random murders along the way). Not to say Robert Patrick didn't do a good job, but Frank Black would have been the true pinnacle of awesome. He was also known to be quite the paranormal skeptic, so would have fit into the purpose of the Doggett character nicely as well as reignited the series and finally give Millennium the respect it deserved.
Of course, if the writers thought about planning even for a second, we wouldn't have the aimless, directionless, WTF-nature of the 3rd season of Millennium or the awful "Millennium" wrap-up X-Files episode. I think they could have saved both series with this simple idea. Oh well.
(Also posting this on the X-Files board)