Here's what I'm guessing.....
Infinite Crisis is going to screw the major continuity up to hell, and the Batman Comics and Superman Comics are being created as a way to keep the more recognizable aspects of the characters for people who might get involved post-movies. I'm not saying they won't be good, but they make sense from a marketing aspect as well as from the fan perspective.
In all seriousness, I don't think Bruce Wayne will be Batman in regular DC continuity... If he survives, he'll take on the role of Oracle. (Barbara's coming back as Batgirl somehow, she's on the cover of Supergirl #3)... He's just put himself into a position he might not be able to get out of. At the same time, they want the Bruce Wayne batman to be kicking arse in Gotham, so they made All-Star.
I also think Lois is going to die... Rawr.
*waits for the uproar*