Rob finds flaws
Wolverine starts off as a great action film. It seems to have Logan (Wolverine) down pat, with a simplified but valid version of Logan's origin. Then the plot questions start piling up.
This is poor planning for several reasons. What if something goes wrong in creating Weapon XI? Then Stryker has an enraged Weapon X and no way to stop him. What if Weapon X kills Stryker before Weapon XI can kill Weapon X? What if Weapon X gets lucky and beats Weapon XI?
I guess Stryker's plan was to erase Logan's memory so he too would be a killing machine for the military. But erasing the memory of someone with a healing factor is a big gamble. Hasn't Stryker ever seen any movies where the amnesiac starts having flashbacks?
Gambit's gambit fails
Logan runs into Victor outside the meeting place. They fight and Logan prepares to deliver the killing blow. Then Gambit blows up the scene and lets Victor escape.
Huh? Logan told Gambit he wanted to kill Victor, and now he's about to do it. Gambit will get his wish of not being involved if he does nothing. By interfering, he ensures that Logan will turn on him and force him to cooperate.
It's crazy. Gambit gets involved when he doesn't want to and helps the bad guy escape. How about letting the good guy take care of the bad guy so Gambit's involvement is no longer needed?
One critic said Gambit was afraid Logan was there to recapture him. But there's no evidence of that in the movie. Logan says he wants to kill Victor and Stryker, not to recapture Gambit.
In any case, Gambit's best bet is to let Logan and Victor fight to the death while he flees. Not to break up the fight so Logan can concentrate on him. It may be convenient for the plot, but it makes no sense.
The big finish involves a lot of fighting, killing, and exploding things. The ratio of characterization to action goes down, which detracts from the movie. But the above plot loopholes are the main problem.
I could've excused the confusion about why Stryker gave Logan the adamantium, but when Gambit started acting irrationally, I started noticing. While I enjoyed the rest of the movie, I spent half the time trying to puzzle out the plot twists. What could've been an 8.5 or 9.0 movie ends up an 8.0.
Another flaw didn't hurt the movie much, but is worth mentioning. Logan is born sometime in 19th-century North America. He and his brother Victor serve together in the Civil War, World Wars I and II (on D-Day, no less), Vietnam, the Gulf War, etc.
None of this ever happened in the comic books, by the way. I'm not sure Logan served as a regular soldier in any war.
Then Logan casually mentions he's a Canadian. I could imagine Canadians serving with US troops in the 20th-century wars, but in the Civil War? I don't think so.
For more on the subject, see Kayla Silverfox in Wolverine and Kuekuatsheu in Wolverine.