Now that MoS is out, I have to say that I would have much preferred Singer's sequel to SR, albeit with some modifications. And given Singer's track record with sequels, I really think going forward with the reboot was utterly pointless. To be honest, SR did decent BO - WB should have just kept their expectations in check. I think the real reason they didn't go through with the sequel to SR was because they wanted to make Superman dark, hip, and modern, and therefore favored a reboot.
This plotline potentially could have gone into Dark Knight territory without actually dumbing down the character - too bad we'll never see it though (unless the MoS series ends up going down the crapper and some other director decides to revive the Donnerverse years later).
One thing I would have liked is Brainiac also bringing the Eradicator program to Earth (yes, I'm biased), and at the end of the film, the Eradicator turns on Brainiac and decides to help Kal-El. The Eradicator manages to get Brainiac out of Jason's body, but in the process, ends up taking over Jason's body permanently. In other words, Jason becomes the Eradicator's bodily host.
Edit: I think the original link at IESB was taken down - for anyone who is interested, that plot outline can still be accessed here: http://www.trekbbs.com/showthread.php?t=133489