I would not like to see Bane, Joker, or Killer Croc in the next game. I think they need to use other villains, there are some pretty cool ones that they could use and make even more disturbing to fit into their verse. Firefly and the Ventriloquist being two I can think of off the top of my head.
Nightwing, Robin (I know it's their design and they have rights to do what they want creatively, but I'd really like a rework of Tim's model. He needs hair, and I think he needs to be slimmed down a bit. Tim always appeared more lithe, like a swimmer's build), and possibly Batgirl (I'd prefer Cas, but Steph would be cool too) stories and side missions. Such as you could have side missions accessible to all of them, Batman included, but you'd get to choose which character you'd play to complete it (don't know how they'd do this but it'd be awesome if they could do unique dialogue for each character during the mission. replay value!)
If Catwoman does appear in the next game, please rework her character. While she is a very flirtatious character, there are many more layers to her personality. I didn't feel like these layers were very well explored.
Phew long post, sorry