The big flaw was The Memento Flaw. IE, waiting too damn long to explain something. In this film, the mutants are mostly gone and Logan isn't doing well. This doesn't seem to be addressed until near the very end. Almost nothing is mentioned about this. No hints at all, that I recall. The explanation then leads to questions of competency of the mutants not seeing this coming and dealing with it. The reveal felt like the anti-climatic reveal of Snape as the Half Blood Prince in the movie.
Poor Eric La Salle, also known as that asshole character from ER. Hey, let's stay over for the night!
Are you fucking kidding me?! You know the people found you quickly the first time!
The death of Xavier. So fake psychopath Wolverine just stands there for how long?! That is a massive narrative cheat. Also Xavier's death seemed to occur almost needlessly and as a convenience to the plot... it'd be harder for Xavier and Logan to be fighting one last time together running in the woods. It'd been better to how figured out how Xavier could have made it to the final battle which could have made the final battle scene a bit more designed than just chop chop. Additionally, much like the Star Wars icon's death in Star Wars VII felt contrived and pointless instead of incredible climatic, this death seemed cheap and confusing. (Why is Wolverine's hair different... oh must be a dream or something... aw shit, this is real.)
Finally, convenience.
- The albino betrays betrays betrays and then does something about it.
- In the wilderness, driving well off-road, but then the Reavers can amass a large wheeled force on a road within the last few miles of the border?!
- They've got drones? Why not plant bombs? Blow them up, mission accomplished.
- Why are they recapturing the kids? Aren't they trying to kill them?!
And most importantly, where in the fuck in North Dakota was Eden?! Desert, tall rock cliffs?! Along the Canadian border? And the spot on the map for Eden, wasn't 7 miles from the Canadian Border, if I recall correctly. Oh, and why in the hell did it matter about the border in the first place? Even the evil military people were worried about the border. What, did Canada become a massive military force in the last 10 years?