As we thought, and as I pleaded, this will become an X-Men Begins but with some returning cast members (McKellen and Stewart at some point).
We need to see Magneto's children choosing to stay with Xavier rather than Magneto after Magneto does something terrible. As in the prequel to X1, Magneto could attempt to kill the 'Dr Death' who murdered his parents, and as in the prequel he could find and rescue Cyclops.
I'd like to see this: Magneto goes off on a solo mission with some of the school students (his children Scarlet Witch and Quicksilver, and Lorelei, Unus and Vanisher) to destroy a prison holding 'Dr Death' and other Nazi war criminals. This leads to conflict with Xavier over using the students like this. Magneto then leaves but he keeps his initial Brotherhood.
Xavier begins to assemble a team in case Magneto does anything else. He has Storm, Jean, Cyclops, Beast, Petra (or maybe Magma instead), Darwin (needs a new name like Adapter), Sway and Vulcan. In their first battle on the island of Krakoa, Xavier is crippled and Petra, Darwin, Sway and Vulcan die. Scarlet Witch and Quicksilver abandon their father, increasing Magneto's bitterness. The island is destroyed by Petra/Magma.
Krakoa could also be reimagined as a city, or a secret facility where Nazi war criminals are carrying on their work. As it also sounds like Krakow, (in Poland) it could be somewhere in eastern Europe.
Not sure if those events are too extreme and dramatic to happen prior to the events of X1, but that's my initial thought.
