Kara's Traditional Origin Doesn't Fit Into the DCEU's Krypton
Regardless of what plans Snyder had and what he managed to set-up in the films he had finished, Supergirl's origins would have to be heavily altered to bring her into the reality of the DCEU. Her classic origin story is incompatible with Snyder's vision of Krypton for several reasons. The chief one is that Supergirl's classic origin requires her to have made her way to Earth in the same circumstances as her baby cousin - an impossibility given the story of Man of Steel.
In the original Silver Age comics, one Kryptonian city - Argo City - managed to survive the destruction of the planet thanks to a dome designed by the engineer Zor-El - brother of Jor-El and uncle of Superman. While he had built the dome to help manage the weather of his hometown, it proved powerful enough to preserve the atmosphere within the dome after Krypton's destruction and the ground underneath the city as well. Unfortunately, the land under them slowly changed into Kryptonite and the lead shielding Zor-El created to protect them was eventually shredded by meteorites. This led Zor-El to use an emergency rocket he had constructed to send his daughter Kara to Earth.
Ignoring the scientific implausibility of a city not being instantly atomized by the destruction of a planet, there is another conflict between the two visions of Krypton. The classic Krypton of the comics is a far kinder place, with family units not unlike those on Earth. Despite their access to advanced technology, the people of Krypton in the comics still behaved in a manner that we would consider largely recognizable.
What little we see of Krypton in Man of Steel suggests a far different society, structured around guilds and houses rather than nuclear families. Children are created through genetic engineering and bred towards specific purposes within Kryptonian society. The idea of romantic and physical love is viewed as anathema, with Zod being visibly disgusted when he learns that Jor-El and Lara Lor-Van gave birth to Kal-El in "the natural way." It is difficult to see Zor-El learning of his brother's plans for his "secret child" and using them to save his daughter in the same fashion as in the comics in this reality, given that there's a fair chance Zor-El might not exist with the same sense of brotherly affection we saw in the comics.
While the image of Kara Zor-El presented in the Man of Steel prequel comic side-steps most of these issues, it introduces a whole host of other problems. The idea of Kara having a boyfriend, her interactions with her parents after her graduation and Dev-Em's plans for Kara once they were marooned together seem to conflict with the Kryptonian ideas regarding love, family and sex presented in Man of Steel. The prequel comic also introduces a massive plot-hole, with each of the scout ships being equipped with a copy of the Growth Codex. Zod's reasons for needing Kal-El and Jor-El's plan to steal the Codex fall apart when you realize there was a copy of the Codex somewhere on the scout ship in the Arctic and that Zod could just as easily have taken that instead of bothering with trying to capture or kill Kal-El. Never mind trying to locate one of the other potential 999 colonies!
Why This New Supergirl Is Probably Different
Ignoring these problems the prequel comic raises, there are many other reasons to believe that we'll see an entirely different Supergirl in the upcoming film. For one thing, few people read the prequel comic relative to the number of people who saw Man of Steel. Given that, it seems silly to adhere to that one story when the problems caused by accommodating it far outweigh the benefits.
Another reason we are likely to see a different kind of Supergirl is the simple fact that Warner Brothers appears to be trying to move away Zack Snyder's DCEU. One need only look at the Justice League movie and the changes wrought by Joss Whedon's reshoots to see how badly Warner Brothers wanted to move away from the darker vision offered by Batman v Superman. Given that and how resistant Warner Bros. is to the idea of releasing a Snyder Cut of Justice League, it seems highly unlikely they would accommodate his plans for Supergirl.
All of this is, of course, assuming the Supergirl movie will come to pass. DC has a long list of projects in development, many of which have been so for years. Having a screenwriter is a strong step, but that needn't mean Kara Zor-El is locked into a big screen appearance. This may be just a spec script, or the whole project could exist in part as a bargaining tactic in WB's contract negotiations with Henry Cavill. What does seem clear, though, is that Supergirl isn't being made with completing Snyder's vision in mind.
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