Came across an interesting article by Screenrant today.
https://screenrant.com/xmen-mcu-cano...tan-lee-story/
Basically, Stan Lee originally came up with the mutant concept before he created the X-men. He wrote a one-off story in Amazing Adult Fantasy # 14 (literally the issue before Spider-Man's debut!) about a guy who suddenly developed powers and tried to use them for good but was hated and feared by humanity. He then meets a bunch of other such mutants who take him away to a hidden sanctuary where all mutants are hiding out until the day humanity at large was ready to accept them.
The article suggests using this story, along with Jonathan Hickman's ongoing Krakoa story, as a blueprint for the MCU X-men reboot by revealing that mutants have been hiding away on Krakoa, which is why the world at large is unaware of their existence. But two factions develop on Krakoa, with one group heading out into the world to conquer it on behalf of mutants and the other group setting out to stop them - leading to the classic X-men vs. Brotherhood conflict.
I feel, of all the MCU X-men reboot ideas I've read, that this one makes a lot of sense! It also kinda fits in with the early premise of Ultimate X-men, where Xavier and Magneto worked together to build a mutant sanctuary and society in the Savage Land first before their falling out and Xavier leaving to start the school.