I don't think they handle the X Men alternate universe/timeline stuff very well in the movies. Does Loan have adamantium covered claws or not? Is professor X alive or not? for me it really detracts from the stories to just keep changing everything up on all the characters. It's like a fancier more expensive Simpson episode. You know when it's over nothing will really be changed since they can just make a new alternate timeline and have everyone back.
It's the same in the comics though. All sorts of heroes die and come back, time jumps, alternate dimensions, Wolverine had bone claws, adamantium, back to bone then adamantium again in the comics.
The X-men story has always been messy. That messiness has carried over. Intended or not.