This is how you can tell the difference between professionals and Josh Trank.
Yeah, I'm not absolving 20th Century Fox for what happened with that production, but Trank is hardly blameless. I am just pointing out that when a director does a big budget film a director will have to be faced with losing entire action sequences, scenes or big moments. As a result, they have to rewrite and compensate for losing those scenes.
In this case, Wernick and Reese lost a big shootout scene. Instead, they were able to find a workaround where OK, they do lose a piece of action, so they make into another Deadpool-esque gag.
Now let's look at X-Men 2. Everyone has probably forgotten at this point, but a crucial scene the film lost was the DANGER ROOM scene. That was a major deal. The scene was written, storyboarded, and even pre-visualized. I think they even began making the set. But at the last minute they lost that scene while Wolverine was at the mansion. So they replaced it with that scene with Wolverine chatting with Iceman, which was a good character building scene for both characters.
Another big thing the film lost? Toad and Toad vs. Nightcrawler. A set was also built for that Toad vs. Nightcrawler fight. Toad was going to be another minion for Stryker. Instead that scene was lost and no Toad in the movie either. Wouldn't that have been cool if the film had that moment? Yeah most definitely, especially because Nightcrawler doesn't get to fight in the second half. But the film is still a good film without it.
Now let's look at something like Avengers. For Avengers, even that film we lost some of Cap's action beats and Whedon wanted another bad guy villain for the Avengers to fight. It happens.
So in other words, doing these big budget tentpole films is rough. You have to make a lot of artistic vs. commercial compromises. However, you still have to be a professional and do your job. Not saying it's stress free, but you have to be prepared to possibly lose some and win some.