Love X-Men, but there’s definitely some changes to be made to make the film look more like the characters from the comics:
The roster would be increased to include Gambit and Beast—Gambit essentially replaces Bobby in the narrative, and Beast takes over from Jean in the medical bay.
Instead of a runaway teen, Rogue should have been introduced as a young adult (early 20s) when she meets Logan in Canada.
I would have given Rogue her classic powers too. When she’s on the road with Logan, we’re treated to a flashback… a woman named Raven takes Rogue under her wing and teaches her to use her powers. Before long, Rogue is manipulated her into using them against another like her—purposefully opaque as to not shown nor directly name-drop Carol Danvers / Ms. Marvel. The experience left Rogue forever changed, permanently absorbing super strength and flight. She fled Raven and her newfound family.
When Rogue is later captured, and Magneto reveals his plan to her, Mystique then reveals herself as Raven. Both she and Magneto have been planning this for a long time, and have been trying to get Rogue back ever since she left. Though she tries to fight the Brotherhood, Rogue’s defeated and placed in the machine.
With another two X-Men, I’d add Pyro or Blob to the Brotherhood as well (probably Pyro).
The mansion should still function as a school but there’s no Bobby Drake. The Jubilee and Kitty cameos remain but other mutant student cameo are non-character-specific powers/effects & physical mutations.
Both Cyclops and Storm’s roles would be enhanced with character-driven dialogue (i.e. Storm connecting with Rogue, teaching her to not look at her gifts as a curse; or Scott stepping up as leader and earning Logan’s respect) and better displays/use of their powers.
Jean too would be less passive and more empowered. I like the idea of Professor X holding her back from using Cerebro but when she finally does use it, although it hurts immensely, she fights through the pain. When Cyclops opens the door to save her, she’s standing triumphant with the information they need.
And lastly, Sentinels. After the mutant chaos at the train station and fearing an incident at the upcoming UN Summit, the President enacts the Sentinel program (which would have been mentioned earlier in the film). After the X-Men destroy Magneto’s machine and save the world’s leaders, they’re still attacked by a squadron of five Sentinels—something akin to the 70s design used in DOFP—driving home that they’re fighting for a world that hates and fears them.