I really don't think this should prevent you from buying the film. There are big differences for sure but nothing that really affects the characters.
-Charles walks in X3 and XOW, but who cares about those films anyways
-If Storm and Cyclops are kids in XMFC, they would be in their late 40s/50s in the new movies but the new films could have taken place earlier than we think.
-Charles says he met Erik at 17 when he met him at 30.
-Beast is human in X2 but it's a teeny cameo appearance and maybe in 40 years he found a very temporary cure. Or is wearing an appearance-changer thing like Kurt had in X-Men Evolution.
-Charles and Raven don't acknowledge each other. They must have had a huge fight, or maybe Emma mindwiped Raven, or something.
-Charles says Erik helped him build Cerebro. In the movie Hank built the FIRST one. It has to get rebuilt at some point, and I can definitely see Erik helping Charles build it in a moment of truce. They're not enemies yet, don't forget.
That's all I can think of at the moment. TBH I'd much rather this was a reboot than a prequel and I'd love it if they just went their own way in a sequel. But I think it's a silly thing to not get it just because you don't like the fractured continuities. :P