5 Ways To Improve The X-Men Timeline
5. Xavier
While this might not solve all of the issues, it is an interesting solution for certain events. Charles claimed in the first X-Men film that he first met Magneto when he was 17 but First Class went on to contradict that. What if some of the lapses in memory, if we want to call them that, are due to him using Beast's serum so that he could walk in DoFP?
This may also be the contributing factor in why he eventually loses his mind in the time before Logan. There's also the matter of Mystique being so connected to his past in the prequel trilogy yet this is never mentioned in the originals. You could even factor in him being blown to billions of pieces and transferring his mind into his twin brother as another reason, even if that does get affected by the time that is changed by DoFP.
If we are to see McAvoy's Xavier for a few more outings then perhaps they could eventually have a scene that mimics what occurred when he had his seizures in Logan. This could be when Beast suggests that it's a side-effect from his abuse of the serum. Again, it doesn't plug all the holes in the timeline but some with regard to Xavier.