Let me Keep this direct and concise as possibe - I am pretty damned angry after reading the details of this script. This script breaks EVERY single rule so far set by comic book movies of staying true and faithful to the comic book counterparts, I don't think a comic character's movie origin has been changed so drastically from the source till now(perhaps Howard The Duck?).
First as has been mentioned the timeline glitch is unnerving as all hell but nobody seems to catch the most glaring outrage which completely cripples the Woilverine character's core essence: HE FRICKIN' VOLUNTEERS FOR THE WEAPON X PROCEDURE! This defeats the entire tragedy and inner turmoil of Logan as a character, being captured against his will and tortured is what makes Wolverine who he is, take that away and you have nothing but a cheezy revenge film with an A-Hole for a lead. I can proclaim that I am a true Wolverine fan they don't come much bigger, and this rape of my favorite fictional character is criminal, Spider-Man decapitating bank robbers in the third movie criminal.