This is how I'd like to see it go, going on the villains I think fit the feel of the new movies:
Batman Begins:
Ra's Al Ghul - DEAD (we won't see him again)
Carmine Falcone - UNKNOWN (wherever he is he's too insane to matter)
The Scarecrow - AT LARGE
The Dark Knight:
Joker - ARKHAM (captured and either put on trial or awaiting trial in a sequel)
Scarecrow - DEAD/ARKHAM (could possibly help Joker get his "venom", either killed (maybe even by the Joker) or captured by Batman)
Third Movie (should be really centered on taking out the crime in Gotham, hence the villains, should have only a few short scenes with Joker/Quinzel):
Two-Face - DEAD/ARKHAM (main villain)
Penguin - JAIL (arms dealer/mobster, maybe helps the other villains, operates out of Iceberg Lounge, captured by Batman)
Fourth Movie:
Hush - DEAD (main villain, killed by Batman)
Joker - AT LARGE (Hush releases Joker from Arkham to help him in his plan against Batman, Joker betrays him since he doesn't want anyone else to kill Batman but him. Joker makes a bloody return to Arkham at the end to get Dr. Quinzel.)
Fifth Movie:
Joker - DEAD? (goes on personal vendetta against Batman & Gordon, seemingly killed at the end of the movie.)
Harley Quinn - JAIL/ARKHAM
Tell me what you guys think. I would have liked Catwomen but I can't see it since that character has it's own series of movies now. And I would want the traditional Selina Kyle, not Halle Berry.