I have not read any of the 'Origins' story with the James Howlett stuff, so I'm just going to go with what was already in the movie, and talk about how I would have improved it using elements from the Wolverine comics I have read, and making my own sh** up.
Ok, same opening with him as a kid, except, stay with that for the first half hour, show him and Victor fending for themselves as they discover their own capabilities as mutants.
Just do an Oliver Twist type of deal, have them survive as thieves, before being taken in by a gang of kid thieves run by a Fagin type, or older teenagers or something. Victor begins to get into the whole villan thing here, finding himself, while Logan is torn between a loyalty to his brother, fear of being alone and caught for the murder of his father, and getting the hell away from this life, that does not feel right to him.
Show some incident with his healing factor being brought into play, showing it full capabilities, maybe he gets stabbed by another kid in an argument, Victor thinks Logan is dead and kills the kid, he is about to take on the whole gang, when Logan wakes up fully healed and back to life, they fight their way out and escape.
We should have seen something like this in the film, the first time Logan finds out the true capabilities of his healing factor to bring him back to life from deadly injuries.
Cut to them as adults in the trenches of the Civil War, which then segues into WWII and the Vietman war, much like the opening credits, except give us dialouge heavy and extended action for the Vietnam sequences, showing us just how psychotic Victor has become as his revelry in his own power has been barely held in check, given free reign completely in this particular war, keep the end the same as we got, with them going to work with Stryker.
eh, I think i'd just do what the film did with the Weapon X team, just show the one mission, but y'know, make it more ambitious, and get Logan involved in the proceedings this time, show him doing something pretty bad/ruthless in the course of the mission(to fit in with Stryker's line in X2 about him being a bad guy in the past), maybe just losing it in a beserker rage and taking out a bunch of those crimainl jewel dealers, where he did not need to.
But, have the same end up, where he draws the line at slaughtering innocents and leaves the team as a result, but in the process he almost kills Victor in the resulting fight.
Now, cut to the same story here with Silver Fox, keep it pretty much the same kind of thing, but, when he confronts Sabretooth, have the resulting fight go on just like in Wolverine issue 10, an extended hunt/fight in the snow covered wilderness, make it go on for about twenty minutes, it should be much like the Vader/Luke fight at the end of ESB, with Victor of course coming out like his namesake.
No plot with SF still being alive, Victor really does kill her, in retribution for Logan betraying him and almost killing him, as he feels he has been loyal to Logan his whole life. He kills SF because in his mind she has taken the place of himself in Logan's affections.
Sabretooth being more outright psychotic, like he was in the early comics.
After this fight with Sabretooth, Logan is pushed beyond where his healing factor has ever taken him before, Stryker comes in to scoop up the pieces, and he wakes up under the knife in the operating theatre getting the adamantium feed into him.
the process takes away all of Logans' memories.
I have not read the BWS story, but I got the gist from the animated adaption and flashbacks in other books, keep it much the same way, with Logan fighting his way out in an animalistic state, before being taken in by the a couple(but not the Hudsons, too complicated to bring in that whole other Alpha Flight story).
Show a montage type deal of him being nursed back to sanity over the course of a few months, with a couple of pivotal scenes, the metal claws being unleashed for the first time when Logan wakes in bed, and 'Heather' calming him down etc.
The military tracks Logan down when a local recognises him when he answers the door at the 'Hudson's'(there are 'Wanted' posters pasted throughout the area saying Logan is wanted for murder, so he is reported when recognised.) They try to capture him for brainwashing purposes.
Logan kills them all, same scene as the movie with the motorbike, and decides to track down this organisation he suspects is responsible for his condition and memory loss.
He gets flashes of memories surfacing(much like in X2), some of the experiment, but mainly those of Silver Fox and Victor.
Following these flashes of repressed memories, he finds his cabin in the mountains where Silver Fox was killed, discovers mementos, photos, and her diary, and pieces together what happened. He gets wind of Victor's scent from the cabin and tracks Sabretooth and the secret military base down. There he frees Gambit, and they both take on a group of mutants, along with Sabretooth, freeing all the captured mutants the government has been experimenting on.
(No cyclops origin here, keep that for an X-Men prequel movie, but have Prof X appear at the end to pick up some of the freed mutants)
Sabretooth escapes, but is hurt badly, at the end of the film, we see Stryker putting Sabretooth through an experimental process, saying he could not withsatnd the adamantium bonding process, but this work will make him bigger and stronger, in a way that will make him a match for Wolverine next time they meet.
He emerges from the process looking much like Tyler Mane did in X-Men1. The process wipes Victor's memory blank, and his appearance is such that it explians why Logan does not recognise him in the later film.
