Usually reboots do the opposite of the series that preceded it.
Well, not necessarily, they just do things differently. Hulk wasn't really opposite of Incredible Hulk. And it's possible the next batman movie won't be a reboot. And even if it was, I don't see how there is any indication that they were going to copy modern batman stories.
Mind you, they probably will lift story elements, like all superheroes do. Lots of stuff was lifted from the Long Halloween with Dark Knight, but no, they're not likely to adapt a storyline in full, new or old.
Personally, I'm holding out hope for Batman Beyond.