I'm very excited for the potential of a story where we get to see Jean and Storm be best friends instead of being told that they're best friends.
In terms of the implications of MoM, I kinda feel like that Illuminati scene was throwing whatever would get fans excited (looking at you Jim) at the screen. They went with that iconic design because it looks cool but I feel like there's little chance that it'll affect the animated show. Shoot the MCU had an entire episode in What If? dedicated to creating and developing an evil Doctor Strange and then they just used another one in the MoM.