Batman is Kirk Langstrom instead of Bruce Wayne. In the comics Langstrom is Man-Bat, one of The Batman's many enemies. The film sees a play on him being less of an actual man size bat and more of a classic horror vampire.
Batman who "only kills criminals" is voiced by Michael C. Hall who portrayed Dexter Morgan a serial killer who only killed serial killers.
Wonder Woman in this film is named "Bekka". In the main DC continuity, she is a minor character and Orion's wife.
According to writer Bruce Timm, the hardest character to redesign and reimagine was Wonder Woman. It wasn't until after bringing up an old sketch that inspiration struck.
During the first flashback (Kirk Langstrom/Batman) Dr. Magnus refers to "Crazy Ivy" who is going to bring her "home grown." This is a nod to Poison Ivy of the main DC continuity, a super villain with plant and flora abilities.
The affiliated scientists to the Fair Play Project are: John Henry Irons (a.k.a. Steel), T.O. Morrow (member of the Injustice League), Michael Holt (a.k.a. Mister Terrific), Victor Fries (a.k.a. Mr. Freeze), Pat Dugan (a.k.a. S.T.R.I.P.E.), Emil Hamilton (member of the Secret Society), Karen Beecher (a.k.a. Bumblebee), Ray Palmer (Atom), Silas Stone (father of Victor Stone a.k.a. Cyborg), Thaddeus Sivana (a.k.a. Doctor Sivana, member of the Injustice League), Kimyo Hoshi (a.k.a. Doctor Light), Stephen Shin (ocasional friend of Aquaman) and William Magnus.
During the flashback scene, Kirk throws away three experimental mice in the trash can named "Mickey, Minnie, and Mighty". A nod to the famous Mickey Mouse, Minnie Mouse, and Mighty Mouse.
The "Vincent Price movie, five letters" which Will is trying to solve in the crossword puzzle is a reference to Laura (1944) (1956), in which Price played a wealthy gadabout involved in a love triangle with the titular woman. Lydecker's (Price's character) jealous love for Laura reflects the triangle between Will, Tina, and Kirk.
When Batman accesses Silas Stone's computer at Gotham University, he finds an email mentioning "Project Fairplay" but also other documents which contain extracts from "The English Mail-Coach or The Glory of Motion", an essay written in 1849 by Thomas de Quincey. One document which begins with "In some of these the custom permitted the student to keep what are called 'short terms'" has been edited to remove references to "Mr. Palmer" (John Palmer, instigator of the mail-coach service in Britain). This is probably to avoid confusion with DC character Ray Palmer who is murdered earlier in the film.