Bear in mind good citizens of Gotham, this is just my personal preference, and I am open to criticism and conflicting opinions.
FIRST FILM:
Mr. Freeze.
Main driving force of the film. At the beginning, Joker takes Victor Fries hostage to get the attention of Batman. Joker is taken down easily and brought to Arkham Asylum. Seeing how intelligent Fries is, Bruce Wayne hires him for Wayne Enterprises.
The rest of his origin story would be from New 52. To quote Wikipedia, " In this new origin, Nora was never Fries's wife. Her name was Nora Fields, a woman born in 1943. When Nora was 23, she was diagnosed with an incurable heart disease, so her family placed her in cryogenic stasis hoping that a cure would be found in the future. Fries, having written his doctoral thesis on Nora, took on a position as a cryogenic researcher and technician at Wayne Enterprises, the facility that housed Nora's body. Eventually, he fell in love with Nora and became dedicated to finding a reliable method for slowly thawing cryogenic subjects. However, Bruce Wayne ordered the project to be shut down, as he began to feel uncomfortable with Fries' obsession with Nora. Furious, Fries hurled a chair at Wayne, who dodged the attack; the chair smashed into an array of cryonic chemical tanks, the contents of which sprayed onto Fries and transformed him into Mr. Freeze."
Scarecrow.
A somewhat minor villain of the movie. Disguising himself under the new identity Professor Rance due to a criminal record under his real name, Jonathan Crane. He simply wants revenge on the world due to the Hell he's received all his life.
Also in this movie, Nightwing is already established (if he's not already in BvS). And Robin makes his debut as either Jason Todd or Tim Drake.
SECOND FILM:
Edward Nigma, the Riddler.
Only real villain of the movie. His motives are to discover who Batman really is under the mask (similar to Joker in TDK). Once he reveals to Batman that he knows his identity, he hints to Batman--through some clever riddle, of course--that Joker told him. When Batman confronts Joker about it in Arkham Asylum at the end of the movie, Joker plays coy.
Maybe Killer Croc could make an appearance as a minor villain ala Two-Face in the Dark Knight.
Also, this film would introduce Barbara Gordon as Batgirl:
THIRD FILM:
Arkham Asylum.
After two films of build up, Joker finally takes over.
The established Bat-family teams up to stop the madness on Arkham. Returning villains would include Scarecrow, and Riddler in a scene or two. Other villains that could appear are Poison Ivy, Bane, Harley Quinn or Zsasz. The story could be based off the video game, any number of comic book arcs, or simply an original story, or some cool combination.
If Jason Todd is the Robin they used, he could be killed setting an "Under the Red Hood" adaption, and Batgirl could be shot through the spine, creating Oracle.
Thanks for reading! Feel free to disagree and tell me what YOU would like to see!