Captain Marvel: What Does The Ending Really Mean?
8. Secret Invasion Probably Isn't Happening As Expected
The Kree-Skrull War forms a big part of the movie, with the Kree wanting galactic domination, but the Skrulls simply looking for a new home. But before we know that, the story leads them to Earth, where they do take on the identities of a few humans, and it's at that stage you start to wonder if this is the groundwork for Secret Invasion.
Secret Invasion is a major crossover event from the comics, where it's revealed that Skrulls have infiltrated a number of the highest-ranking positions on Earth in preparation for a complete takeover, including a few Marvel heroes themselves. It's been widely speculated that the MCU was going to adapt Secret Invasion in some form, which would sense with Captain Marvel laying the groundwork. For a long time now, it's been not just theorised but expected that this would set it up for further exploration in Phase 4.
That would work fine with the Skrulls as you expect them: villains intent on taking over the world. But here, they're extremely sympathetic. Talos is an absolute banter merchant, but he's also a decent being who just wants to do right by his family and the Skrull race as a whole. They're men, women, and children who don't want to fight, but just want to be home and at peace.
It's not completely impossible for Marvel to pull off Secret Invasion from this point though. The film does leave us with Talos' daughter watching her father fight and even suffer at the hands of the Kree, which might mean that when she grows up, she could take the Skrulls towards the villainous route initially expected, and showing a proper version of the Kree-Skrull War. It's difficult to get right, though, since they've been made so sympathetic here, requiring a big swing for it to happen.