As we know, Batman 3 (working title) will be Chris Nolans last Batman film, and he has been quoted as saying that it will 'be an end.' Some have speculated that it will be an ending such as Bruce/Batman defeated or dead. Yet some still see it as hyper-realistic and only as such. I don't believe either to be the case.
Even with Nolan considering this as an ending it's probably more of his way of saying "I have a particular story arc that I'm telling, anything outside of this arc is not important, we can get to the next story arc when we get there."
As for the current Bat-series being hyper-realistic and it's current inability to flow into a possible JLA universe, so what? Like others have stated, a new team will come in and pick up with Batman where Nolan leaves off and will take it in the direction DC desires. I'm not saying it needs to turn into Batman & Robin, but we need to see Batman's transition into a larger world and his enemies, allies, and city all need to show it.
The great thing about the Batman franchise is that it's never the same, and in a good way. Like the comics we get to see all sorts of incarnations of Batman.
This may be the age of the re-boot, but let's not stay in this stage or nothing greater will ever be accomplished.