As for the OP, *if*, in the 80s when it all shook out, Rogue had accidentally stolen Carol's powers permanently, and after Xavier off-loaded the stolen memories back to Carol, Carol went on to become Marvel's answer to Amanda Waller, the non-powered government liaison between the hero community and the authorities and Rogue had eventually come to accept the mantle of Captain Marvel, then that would indeed have been an intriguing spin on things, particularly if, as Captain Marvel, she spent some time as an Avenger, as well as an X-Man, serving like the Beast or Quicksilver, as one of those bridge characters that flits back and forth and helps tie the world together and make it feel less like hero stories set on alternate worlds entirely.
She'd be an interesting Captain Marvel just because her personality is so different, and I could see the government in particular having a lot of trouble with her, *especially* if Carol Danvers ends up being the government authority who 'handles' interactions with the Avengers, etc...
It could make an interesting 'What If?' someday.