I know I would have done a few basic things for this movie.
1.) Extra Characters. Cut down on all the extra characters. Yes, Gambit, Cyclops, Emma, Deadpool, Blob, they're all cool, but they don't belong in this movie. (And it's just weird thinking that Gambit is going to be around 40 during the normal X-men movies) The only extra character out that I would keep would be Deadpool, and if I did, he would be the only Weapon X character besides Wolverine and Sabes that go any character development of much attention.
2.) Weapon 11=badness. Cut the idea that they only used Wolverine to create the "super weapon" Deadpool, and make his experience at Weapon X much more horrific. Show some of the brutal things they do to him, how they almost succeed in making him literally nothing more than a puppet they can control, basically, show some of the amazing evil things that the Professor and the Weapon X program do to Wolverine in the "Weapon X" story by Windsor-Smith.
3. Mindwipe-This goes along with 2, since his mindwipe was part of the things they did to him. But, have them try to mindwipe Wolverine during the process, but have it be like the comics. Not complete amnesia, but partial, where he can't remember much, but he can remember some.
4. Animal Vs. Man-actually show us this struggle. We had lots of lines regarding this "you're not an Animal Logan" "Embrace the other side, Become the Animal," But it fell flat, because we never see Logan exhibit a battle with his feral side. He never comes off as a man who has a dark part to him. Have him struggle with it more, show how he actually enjoys some of the missions he goes on for Weapon X.
5. Brotherly Love. Focus much more on the relationship with Sabretooth and Wolverine. We got nice snippets of Sabes personality, but I wanted to go more in-depth with their interaction. Have Sabretooth be the main villain too, no crappy DP ripoff for the last fight.
Think of how much more shocking and twisted it would be if you found out Sabretooth was one of the people who helped capture Logan and reccomended the torture he had to go through during the Weapon X process to turn him into a killing machine. It would make sense as well. All throughout the Weapon X storyline by Windsor-Smith, they essentially try to torture Logan physically and mentally to strip him down to nothing but his killer instincts. Sabretooth would want that, because it would finally make Logan like him