Captain Marvel is the second feature-length prequel in the MCU, and as with most prequels, it had a big task on its hands.
While Captain America: The First Avenger only had to tell the story of Steve Rogers and how he wound up in the present, Anna Boden and Ryan Fleck's film had to tie heavily into the established canon. The nineties setting was deliberate, and it enabled Marvel to answer some of those unanswered questions that have pervaded the MCU for the past 10-or-so years.
Elements from the Avengers, Captain America and even the Guardians of the Galaxy are all broached, but the film also sets up quite a few events and storylines we haven't yet managed to see on screen. It all feeds into Marvel's wider strategy to mount a 'distinctly different' version of the MCU from Phase 4 onwards, and with Captain Marvel leading the charge, it's only natural that her origin film would help set up some of these events and storylines.
Some hints were obvious, while others were slightly less-so. Either way, Captain Marvel has already proven itself to be a vital addition to the MCU timeline, and will likely influence further films to come...