In a piece discussing Whedon's exit, Variety reports that the premise had already been laid out, suggesting that perhaps the bigger problem was finding a way to stretch a short story into a feature-length film, and to contextualize it within the existing DC films.
"The movie was to be based on the Batgirl story that was first unveiled in DC Comics in 1967, when Barbara Gordon, the daughter of Gotham City police commissioner James Gordon, appeared as the character in 'The Million Dollar Debut of Batgirl!' by writer Gardner Fox and artist Carmine Infantino," Variety reports.
In the story, Barbara Gordon -- a librarian and the daughter of Gotham City Police Commissioner James Gordon -- first appeared as Batgirl and squared off against Killer Moth, who was targeting Bruce Wayne. The story featured a team-up with Batman and Robin, although neither Killer Moth nor Batgirl realized that Batman and Bruce Wayne were one and the same.
With a Nightwing movie also in development, it seems likely the Batgirl film would likely have excluded Robin, been a flashback, or else had to rework the team-up element a bit to allow for the introduction of a non-Dick Grayson Robin character.
Before the project imploded, it was said to be drawing significant influence from the "Batgirl of Burnside" era of the character, begun in 2015, in which Barbara Gordon was played as a bipster and her Batgirl costume reimagined as a kind of patent leather biker outfit with a cape and cowl.
That version, which launched as part of the short-lived "DC You" publishing initiative in the comics, was overtly feminist, and DC You as a whole put emphasis on representation of women and minorities in a way DC had not done in years.
Since the end of DC You and the start of DC's Rebirth in 2016, Batgirl has had a female writer. In the context of the feature film division reportedly seeking a female filmmaker to succeed Whedon, it could be that the influence of more modern Batgirl stories is simply overtaking the influence of Silver Age tales like "The Million Dollar Debut," which was published in 1967 and was written and drawn entirely by men.