Captain Marvel will NOT be set in the Marvel Cinematic Universe's present-day. At Marvel's big Saturday presentation at SDCC, the studio revealed that Captain Marvel will be set in the 1990s.
While we don't know why Captain Marvel will be a flashback movie, it does explain one of the reasons why Samuel L. Jackson is in the film. It was announced that Nick Fury will appear in Captain Marvel AND have both his eyes.
This also puts into context a comment Nick Fury made way back in 2008's Iron Man. "You think you're the only superhero in the world?" Fury asked Iron Man before recruiting him to the Avengers Initiative. Mr. Stark, you've become part of a bigger universe. You just don't know it yet."
It looks like Captain Marvel could be the superhero Fury was talking about.
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