How about the acts of vengeance?
Unlike a Masters of Evil movie (which would require more of a team dynamic, and thus require 1 major villain and a bunch of henchmen) The Acts of Vengeance was a team of big hitters, who got together and switched enemies. An Acts of Vengeance style plotline would also keep the film from getting cluttered with 12 characters on the screen at once, since it would be more a one on one series of battles.
A link for those of you less familiar with the plot line.
Dream MCU phase 3:
2016: Thor: Ragnarok, Doctor Strange
2017: Captain America: Secret Empire, Black Panther
2018: The Incredible Hulk: Rise of the Leader, Guardians of the Galaxy: War of Kings
2019: The Inhumans, Avengers: Thanos Imperative