Ok, I just want to start by saying I liked this movie. Yes, it messed up a lot of things from the comics, and several characters were butchered from their original versions (especially the beloved Deadpool). However, I think much of the film could have been redeemed simply by changing the ending. So here's my take on how it should have gone down.
The original ending (for those who have not seen or have forgotten) shows Logan showing up at the Three Mile Island facility, confronting Striker, walking away (WHY???), rejoining his girlfriend, freeing a bunch of mutants, briefly confronting Sabertooth, then teaming up with him to fight a very screwed-up and mind-controlled Deadpool before decapitating him and getting shot in the head to lose his memories. Yeah, kinda jacked up when you think about it.
Logan SHOULD have shown up and confronted Striker like in the film, but then Sabertooth prevents him from killing Striker. Striker then lets Deadpool loose thinking he will fight for him (no arm blades or mind control melarky), but Deadpool instead wakes up deformed and pissed. He stabs and wounds Striker out of anger and goes completely nuts. In the struggle, he rips open his mouth that Striker had sealed shut, leading to further disfigurement and general craziness.
Cut back to Wolverine and Sabertooth. The fight is waning as Sabertooth loses his resolve from Striker's double-cross. Deadpool comes crashing in, crazy and spouting his famous ridiculousness, and he starts screaming at the two of them and blaming them for everything: leaving him, allowing Striker to mess him up. He goes berzerk on them, and they are forced to join forces against Deadpool, whose only powers are healing and teleporting. That alone would make for a good fight, and much better than the original simply by letting Deadpool spout his ludicrous dialogue that fans love him for.
Eventually Sabertooth and Wolverine enlist the help of Cyclops and Gambit to take down Deadpool. Cyclops and Gambit keep Deadpool suppressed while Wolverine and Sabertooth close in and decapitate him, similar to the original kill in the movie. Striker shows up after the others disperse and shoots Wolverine in the head and the end plays out simlar to the last few minutes of the original movie. However, the end credits scene is Deadpool picking up his head, looking into the camera and saying "What are you lookin' at???", breaking the 4th wall and ending the movie like a boss.
What do you think? Lemme know in the comments section!