I mean you don't watch the films for a groundbreaking story, the action will always take priority because it's a superhero vs supervillain trope, the story definitely helps but will always be stereotypical given how comic books invented most stereotypes...
You wouldn't compare Marvel films to a film like Memento or to a trilogy like LOTR, it's primary focus is more cliched in that regard.
Comic books are interwoven with unique storytelling but in all honesty, there are just as many plot holes as there is story given how many multiverses and timelines there are for each and every character, they can only take so many creative liberties when making a film based off of a comic book.
Still, I think we can agree it is still fantastic entertainment regardless of the criticism. :)