I think I've pinned down what bothered me so much about CAPTAIN MARVEL as a Marvel origin story.
IRON MAN(s) was about someone with tremendous power suddenly realizing the obligations that power implied, and trying to meet those obligations.
THOR, similar. He starts out with tremendous power but also tremendous arrogance, and is stripped of the former while he learns to deal with the latter.
CAPTAIN AMERICA TFA was about an already good man (whose character we were shown) being given the means to be that hero.
GOTG was about a bunch of a-holes becoming reluctant heroes, but also growing in the process.
DOCTOR STRANGE takes an arrogant genius, breaks him, and puts him in a place where the only route to great power is by un-learning some of that arrogance.
Basically the point I'm getting at is: these are all origin stories, not just of SUPERheroes, but of superHEROES. They tell us why we should treat these people as heroes, how their virtuous or heroic character comes to be.
Except for Cap, who is the reverse: someone who is a good but puny man who is finally given the means achieve what he was always trying to do but couldn't on his own.
CAPTAIN MARVEL, on the other hand, shows us absolutely nothing like that. The theme of the film is basically "the power was inside you all along". And we're not really shown anything that leads us to expect her to act heroic.
The character experiences an arc... sort of, but without any discernible or strong motive for the arc.
So, yeah. We're not really shown why she's a hero, or why she became one. She just sort of all of a sudden starts doing vaguely heroic things.
Her defining character trait is "all these men told me I couldn't do it but I still did". Which is great, I guess, but not in any way heroic. So the transition seems kind of forced and out of left field.