To be fair, guys, Tim Miller doesn't ever speak about wanting 100% creative control, and aknowledges that, of course, the producers had final cut. He's merely talking about having a certain amount of control over his movies, being the credited director, which means he probably didn't get enough of it.
There's a difference between wanting final cut (which is not what he's talking about) and wanting to have the possibility to make creative decisions, instead of becoming a mere "executor" on set.
And honestly his original idea to have humanity lose, with time travel being the only option would have brought much needed diversion to the franchise, and it would have upped the stakes, because as he says himself, it would've been a "last stand." And after two movies, that's actually what you need.
There probably were big disagreements during development and pre-production, with the editing phase just being the icing on the cake.
I honestly don't agree, as I think it's a pretty simplistic take on Tim Miller as a director. Because with the script "Deadpool" have, he could've thrived in "trends" and could have made it flashy to a fault --- which he didn't.