If they debut Joker as a minor 'Hannibal' role while locked up in Arkham, perhaps his shrink could also be another minor character who ends up succumbing to Joker's 'logic', and ends up playing a role in freeing him at the end (or after credits sequence) for the next (and perhaps final) movie, where Joker is the villain (with Harley by his side).
I'm curious to see how they'd do Harley on the big screen though, ya know, without making her annoying, unbelievable, and out of place. They have to justify why she's there. Perhaps the of the main focuses/premise of the movie can be regarding the joker's influence, and Harley can be used to best illustrate that. Perhaps in this set of movies, there will be Joker followers/emulators, etc. Harley is just the best example of that, having spent so much time digging around his brain.