Well to be fair they are part of a planned ongoing series of movies. While shared universes are not a thing Marvel invented they were probably the first to start out with a plan on having an ongoing story over 10+ movies.I think it can be boiled down to two reasons:
1. Unless a movie is part of a planned trilogy like LOTR for instance, then the movie itself should be good as a conclusive standalone. When they made The Terminator in the 80's, it was more than good enough as a standalone film. There was not any real need for a Terminator 2, even though that movie arguably is better and does in no way ruin the first film. Marvel is essentially trying to keep people hooked indefinitely. Some of their films feel like long chapters in an ongoing comic book series.
2. It really screams "we have feck you money" when a studio can "predict" the future. Before, when an original blockbuster with sequel potential was released, studios generally wanted to see how well it does before committing to a sequel. Adding a bunch of stuff to an already expensive movie that only makes sense if there's a sequel was probably considered a bad decision. But Marvel are so confident in their success that they can commit to this. It's as if failure isn't even considered to be an option. And in their defence: they are right!
On the second point it might seem like that now but before the Disney buy out Marvel basically risked everything trying to start a shared universe of movies. I think they had released 4-5 movies before Disney bought them. I remember reading they financed the first movies through a $500-600m loan using all their rights as collateral. Had those first few bombed Marvel Studios probably wouldn't be a thing anymore, all their characters would be owned by other studios.
And while Marvels movies are obviously not to the tastes of everyone other studios with more famous characters like WB and Universal have shown that creating a cohesive story over multiple movies that are financially successful enough to warrant it continuing isn't exactly an easy task. Yeah with this approach no doubt the directors lose some independence and creativity being more like the Directors on a TV show where they come in and are given a general outline of what is expected of them. I've never read comics myself but for the medium of comic book characters I imagine it's the best approach for bringing them to the big screen as that's how the comics were so successful. Presenting a group of characters in an ongoing story.
To an extent these Marvel movies are something new, they are more like a massive budget TV show dressed up as Movies. So I can see where Scorsese is coming from to be honest, I don't think he meant his comments to be as critical as a lot of people interpreted them.
