The reboot and all future Batman films should follow a loose continuity similar to the James Bond films IMO. I think we've reached the point where you can pull that off with Batman. Heck, I would argue you don't even need 1 or 2 villains per film anymore. You can do a Batman movie with multiple villains being used (as either major or minor villains) similar to many story arcs in the comics and to Arkham Asylum and Arkham City.
Also, I want to see "The Goddamn Batman" adapted onto the big screen. I'll explain what I mean by that. There are two versions of Batman that writers generally write. The first one is more of a realistic take on him like in Year One, The Long Halloween, and the Nolan films. This Batman is a vigilante that is an extremely skilled man that pushed himself to the limits to do what he does and to take out mobsters, drug dealers, and more grounded supervillains like the Joker, Two-Face, Riddler, etc. Then there is "The Goddamn Batman". This Batman is a man that pushed himself to the limits and beyond and became something that isn't just human, despite not having any superpowers. This Batman is the scariest and most dangerous living thing in the world. He is a prep-time monster. He is capable of defeating anyone, including the entire Justice League, as long as you give him a little bit of prep time. He is capable of going 3-4 days with no sleep or rest and is still capable of fighting at human peak level. He makes even the strongest superpowered heroes shiver in fear. This is the same Batman that makes people like Guy Gardner and the White Martians afraid. This is the same Batman that can pull plans and other things out of his *** and when asked how he was able to do that, someone else says "He's Batman!"
The Batman films we've had so far, specifically the Nolan films (minus TDKR which I disliked), did a good job at adapting "Batman" onto the big screen but we have yet to see a movie that adapts "The Goddamn Batman" onto the big screen. I think the reboot is the chance to do that especially since the possibility of the reboot being tied in to the JL movie exists.
That's what I personally want to see