In trying to think thematically, like a writer/director, there's a way that a Court of Owls story could definitely work in the sequel. Basically, after the flood, the future of Gotham now hangs in the balance. It has the opportunity at a fresh start, can be something new, different, better, etc. So, in a movie in which the FUTURE of Gotham could play a big role, it would make thematic sense to simultaneously dig into its PAST. As in, an examination of sorts as to how it come to be so bad, corrupt, etc, and then reconning with that, not wanting to repeat past mistakes. Plus, you know that in the wake of the flood, when "the system," as secretive and in the shadows as it might be, is being threatened like never before, the Court of Owls would fight tooth and nail to keep their power/influence. But now they're up against an adversary they didn't have to face before; not just Batman... Bruce Wayne. Who is no longer a recluse, but a public figure now hell bent not just on cleaning the streets (via Batman) but rebuilding the them as well, via Bruce.