Yea I'm talking about him leaving Weapon X after they experiment on him, then eventually having to take on the rest of the team.
They could of done the whole film involving Weapon X. Have them out on a few missions, and maybe have Logan not doing so well or just wanting to be better(adds the more darker animalistic touch to him). He needs to get that extra edge so agrees to the experiment. They try to wipe his mind but it goes wrong, he escapes, goes on the run. Stryker then sends Team X to hunt him down. Have a couple of individual battles with a couple of the team members and Creed, Logan finds out where Stryker is, he wants to go finish it once and for all. He then finds himself up against Deadpool (proper Deadpool, costume, healing factor, Zero's gun powers, teleporting) they have a epic fight then Creed comes to his aid as he doesn't want anyone else to kill him. Deadpool spazzes out or something, the cancer (which would of been explained in the film) starts to react with the healing factor.
But before Logan can take care of Stryker something happens to him, Stryker uses his son to wipe Logans memories or something like that.
That's how I would of done the film. Well, sorta like that.