New Mutants spinoff in the pipeline and scheduled for release in 2020, the film is expected to have few (if any) direct connections to the X-Men prequel series that Dark Phoenix belongs to.
As a result, Kinberg's directorial debut (which he also wrote) was ultimately tasked with tying off any and all dangling plot threads from Captain Marvel, Kinberg has compared it to another Marvel Studios film altogether.
In a recent interview with i09, Kinberg likened Dark Phoenix's original conclusion to Civil War, in the way that it split up and pitted the X-Men against one another over their differing opinions about what to do with Jean Grey/Dark Phoenix (Sophie Turner). He itted there were some similarities to Captain Marvel too, though he feels they were fairly minimal in comparison:
My original ending didn’t have the entire X-Family together the way they are in the film now. More than Captain Marvel, you could see a lot of Civil War in that ending. Usually, these big, huge action movies have the climactic moment in the third act. I loved the way that Civil War had its big action action set piece where everyone’s facing off more towards the end of the second act rather than in the third, so that after that huge battle, you’re left with Winter Soldier, Captain America, and Iron Man.
It’s this telescoped down view of their raw emotions, and I loved how intimate that was. That’s what I was going for with Dark Phoenix’s ending even though it then might have looked like Captain Marvel for about two minutes.
Kinberg previously confirmed that Dark Phoenix's ending featured a battle in outer space, before it was moved to a showdown aboard a military train. McAvoy (who once again plays Professor X in the film) later added that there was a "lot of overlap and parallels" between the original ending and a fairly recent superhero movie, which seemed to indicate that he was referring to Captain Marvel (which also ends with a battle in space). Based on Kinberg's latest statement, it seems he may've really been talking about Civil War and the way it too explored a schism within a community of superheroes. What's curious is that Civil War hit theaters more than a year before Dark Phoenix began production, so (in theory) the parallels shouldn't have come as a huge surprise. McAvoy appeared to suggest the similarities were unexpected, but it's possible the overlap between the two superhero movies simply didn't jump out as much until Dark Phoenix's initial cut had been assembled.
Whatever the case may be, Dark Phoenix's reshoots ultimately resulted in some significant changes to the film. Unfortunately, It's difficult to say if they were for the better or worse. Early test screening reactions to Dark Phoenix were reportedly poor, and the final movie has since earned the worst Rotten Tomatoes score for any of Fox's X-Men films. Still, Dark Phoenix's theatrical cut is pretty character-driven for a modern superhero tentpole, and the original ending would've been in keeping with that approach. So, although things changed in the end, one can understand what Kinberg was going for with with Dark Phoenix's original climax.
Source: i09