You're making it sound like a run has to improve the world of comics somehow to be considered a run. If that was true jeph loeb would have been executed. Or at least be out of a job.
It makes sense to me. Trying to cram decades of mythology into a 90 minute movie is just bad film-making. Not to mention the restrictions you have on the character due to the nature of comics themselves.films are adaptations made from something big, forgetting the big thing itself and recognizing it's fragments as the original does not make sense to me.
For one, character development isn't really allowed. If batman suddenly got over the death of his parents, or the punisher was like oh well maybe I am a little crazy, then it has a negative effect on anybody that just wants to jump into a comic and be familiar with what is going on. This sounds insane, but remember that most self-proclaimed comic fans don't read comics. They grew up with the 90's cartoons, which weren't bad at all, but imposed an image of these characters in the minds of children everywhere. Worst of all, it made people thing gambit was cool.
When making a film that is meant to reach out to these people, you have to adhere to that image. For instance trying to make gambit cool when he clearly isn't.
For two, films typically need to adapt the stories to a real world setting. I'm sure you wouldn't argue that Spider-man lives in anything that resembles our world with fucking lazer guns and space planes. Comic book logic can still apply, but films don't have years of back comics to pull recognizable ideas from. If you saw Reed Richard's sonic gun thing in a comic it'd be typical. If some dude pulled it out during a movie without explanation it might be kind of weird. And some things in general just don't transfer well to reality. See: that dragonball move or gambit being cool.
Lastly a comic film is going to be inherently limited for obvious reasons. You can't have Tim Drake just show up in the next Dark Knight without some sort of explanation, and you couldn't pull of something like Batman RIP which pulls all sorts of stuff out of Bman's mythology and history. Superman's Red Son wouldn't work as a film, most likely, without a buttassload of exposition because it assumes that the audience knows too much.
I think we're getting sidetracked here when really what I'm trying to say is that gambit is just really not cool. You mentioned the films being reduced versions of a greater story. That's what every run is. It's a fragment of a character's mythology. You also mentioned "missing the big thing." What's the big thing? A decades old library of previous movies about the character? That's what doesn't make sense to me.