bit of a shame cause Fire & Ice which would be amazing fun to play around with story wise heroines, you have Crimson Fox which could be one heroine or three. Doctor Light, Big Barda, & the Heroines from the Legion of Super Heroes (should time stuff take place.) and that's just Justice League. From the Batman List, you have Batwoman (again three heroines portraying one entity.), From Batman Beyond (yay more timey wimey stuff.) Aqua Girl.
for the record skipping what's already in the game. Also Skipping individuals with no powers or defining characteristic(I.E. Robot, Cynth, etc...) . Also Skipping Royal Flush Gang due to the many many iterations which is shame cause there are some good ones. Finally Skipping Static shock because the game completely skips it same goes for some of the villains for Gotham Girls.
Then we get into everyone's favorite category Female Villains which dear god there's a lot. Just from Batman you have (skipping Baby-doll cause Just NO.) EmmyLou Brown, Calendar Girl, Randa Duane, Phantom, Red Claw, Roxy Rocket, Talia, & Thoth Khepera(tossing this one in as a joke.). From Superman you have Darci, Lashina, Mad Harriet, Mala, Stompa (if your into that kind of thing :/), & Volcana. My Personal Favorite Batman beyond (fair warning timey wimey stuff) you have Curaré (this would be a fun one to play with artistically.), Cynthia, Dee Dee (harley's crazy twin grand daughters. oddly they have red hair and lex before he went bald had red hair...), Freon, Inque, Tigress. Finally Justice League this is the biggest female Rogues gallery, Aresia, Circe, Doctor Cyber (again a character that can be played with.), DreamSlayer (yet another for the artist to have fun with.), Lady Lunar, Morgaine Lefay (yet another one for the artist to have fun with.), Night Fall, Queen Bee, Rampage (if your into that kind of thing I guess), Silver Banshee, Paran Dul, Tsukuri, Shifter, Plastique, & Emerald Empress (Yay more timey Wimey stuff!)
But yeah there isn't a lack of females to toss at the game if you seperated Teen Titans or Young Justice from it, it's just if done right you could have everything and more. because the DCAU is stupidly forgiving with the amount of dimension and time hopping it does that you could literally half ass write something in and it would make sense, the trick is knowing what you can get away with and how much you can get away with.
Edit: take note that is not all the characters I could of listed, I could of also listed Law Enforcement, Military, and the metric Eff ton of girls from Batman & Batman Beyond.