Just an idea for the Batffleck Trilogy if he is planning it and ends up doing it with G. Johns
Batman vs Riddler
a) since Affleck's awesome at detective stuff and he's interested in doing a detective Batman, which differentiate from the TDKT.
b) introduce the Bat family - Barbara, Gordon, Alfred, Fox.
c) have Gordon, Harvey Dent and Bat working together.
d) Riddler story where he's trying to outsmart Batman.
e) have a physical threat, Deathstroke is in, so have a subplot for the person trying to kill Bat. Amanda Waller? Huge Strange? etc.
f) cameos - Deadshot and Harley Quinn doing bad things together, Joker cameo, Bat v Killer Croc, etc
Batman 2 - vs Two Face
a) Harvey transforms into Two Face early in the film, and becomes THE mob boss of Gotham. Two Face lived for 5min in TDK, and Affleck's great with mob stories too, so this would be down his alley.
b) introduce muscles like Bane, Scarecrow etc
c) introduce Catwoman
d) SS cameos - Poison Ivy, Katana etc
Batman 3, vs Joker
a) Batgirl -> Oracle? Gordon's arc. Batgirl can be moved around Bat and SS universes.
b) ties up to Robin storyline
c) bring Harley in, she might have broken up with Joker by now, might help out Bat by putting some psychiatric stuff on the Joker.
and might leave out Penguin, Ra's, Hush, Clayface, King Shark, they could be used in SS. The beauty of shared universe is that all great rogues who don't make it can shine in SS.