The Walt Disney Corporation will always be "the establishment" far more than Scorsese ever will be. Scorsese's movies are on par in terms of hits/flops so in terms of power dynamics, Disney/Marvel is in a position of power over him and other film-makers. The directors of the MCU whether it's James Gunn, or others, despite their youth now have a greater level of power than he does. And yeah that applies to Gunn even after Disney temporarily fired him. When Gunn got fired, he immediately got a huge gig and big pay for The Suicide Squad...when Scorsese as a young man was fired from The Honeymoon Killers he had to go through four years of "director jail" before he got his break.
Scorsese would be "the establishment" as an American mainstream film-maker to say a director out of film-school, or film-makers from other countries like Argentina, China and others who Scorsese at various times has helped. Just this year, he helped the director of The Current War (
https://variety.com/2019/scene/news/...in-1203379557/), the Mexican born Alfonso Gomez-Remon regain final cut from Harvey Weinstein who tried to cut the film (because Weinstein likes to rape movies too). To them Scorsese has been a friendly establishment but that's only a small amount of power he has.
Well it's hard for there to be true real emotional stakes once you make it clear that no matter what the movies will keep churning, the setting will remain standing in such a way that nothing sticks and lasts. In that respects, the MCU is quite like the comic books.
For anyone schooled in cinema which for the vast majority of history and the vast quantity of movies has always meant one-and-done standalone stuff whereby movies end with changes that last stick and are undone...this stuff would look jarring. As Scorsese said, "they are sequels in name but remakes in spirit". In that the story will always be wiped clean in the next movie or one after and start from scratch again.
When the MCU came out, it had a charm of seeing an approximation of comics continuity in live action and it was
refreshing but now it looks like one of the advantages and virtues a superhero movie had which was a sense of definite resolution and change, is being removed. Look at Batman 1989 where Joker dies at the end, or Norman Osborn dying at the end of Spider-Man 1 or Ock in Spider-Man 2. Now you aren't going to get that since studios will want to do a Sinister Six movie or something eventually. So in that respects superhero movies went from cinematic takes on comics to becoming less and less cinematic.