I'd love to see a slightly more "fantastical" take on Batman. I mean, he exists in the same world where a boy crash landed in Kansas from a distant planet. Give us some of the more bizarre villains like Man-Bat and Killer Croc. I'd love to see a very emotional redux of Mr. Freeze ala BTAS's "Heart of Ice" also
If were talking a trilogy here, I'd say Mr. Freeze and the Penguin (as some sort of a insane mob boss arche-type) is the first film; The Riddler and Black Mask in the second; in the final The Joker and I think either Croc or Clayface.
Clayface without a doubt should be the first villain. It allows him to get his detective on, allows for some pretty great imagery, and it provides an unrealistic villain, therefore a polar opposite to the Nolan films.
Mr. Freeze. just as he is in modern comics/games/TAS. Little darker & more serious. Clayface. realistic take like his debut in the comics. Not a monster. Killer Croc. realistic take like in Azarello's Joker. Henchman for the mob. Poison Ivy Hugo Strange Black Mask Riddler Penguin
No Joker until the end of the series, hype him up with Harley Quinn.
None of the other rogues Nolan touched (Bane, Ras/Talia Al Ghul, Scarecrow, Two-Face, Catwoman, Mr. Zsasz, Falcone, Maroni, Daggett)
No Ventriloquist, Hush, Mad Hatter, Deadshot, Solomon Grundy, Man-Bat. I just don't have an interest in seeing them.