As-is, yeah, Captain Marvel is 100% the same character at the start of the movie as she is in the middle of the movie, as she is at the end of the movie. She has a mystery sidequest that seems intended to carry the movie, where she remembers that she was a kid once and that she's Human, but the movie completely spoils that mystery for the audience, so Captain Marvel's the only one who doesn't know. And the not-shocking revelation doesn't really change anything about her. It's kind of worthless in that configuration.
But if you rearrange her story into chronological... Carol's a girl who keeps on falling, but she keeps on getting back up and aiming higher next time. A powerful older woman finally gives her a chance to prove herself and fly a plane when the men won't because of her gender. The mentor dies and leaves her legacy to Carol. Moments later, Carol sacrifices herself, destroying it to keep it out of the hands of the enemy, and in the process becomes Captain Marvel. But the bad guys capture her and brainwash her and now Captain Marvel is working in the service of the obvious bad guys from Guardians of the Galaxy 1. The audience knows it's wrong, regardless of previous Marvel experience. Maybe keep some ambiguity about how maybe the ground-level troops aren't bad guys, maybe they're just pawns, and maybe they might not turn against Captain Marvel. She gets separated from her group, meets Nick Fury, and eventually discovers that maybe the Skrulls aren't the bad guys. Then the AI brainwashing tries to tell her that it's the strong one, it's the one in charge, and she's too weak to fight it (should the AI be male? I'm thinking it should have been male), but Carol says that while she falls sometimes, she always gets back up again, and she kicks her brainwashing to the curb and becomes full superhero.
It's like, across the entire movie, Nick Fury had a story arc. He clearly changed as he interacted with Captain Marvel. But the Captain Marvel he interacted with was mostly static and unchanging. But if Carol's story was extended into the past (rather than her past being relegated to flashbacks), then she has the opportunity to have a complete story arc, while Fury has a differently-timed story arc in the same movie, that takes place during the limited window where he was interacting with Captain Marvel.
I think that in a chronological rearrange, Captain Marvel is an aspirational character to look up to. As-is, the aspiration is there for people who go looking for it, but she's mostly aspirational because she got bitten by the radioactive spider, which is the part that RLM seems to have a problem with. People shouldn't look up to Captain Marvel for her powers, they should look up to her for her character, and I think a rearrange of her story beats would present her character better.