Oh lordy, this would be. . . exceptionally tricky. I can't really give a full, coherent take because there are so many contradictions with current stuff Marvel is doing, not the least being the inhumans plot in Agents of SHIELD. If you asked me a year ago, this would be a lot easier.
Still, some suggestions:
1. Be brave. Be courageous. Write plots that don't depend on humanity being singularly, irrationally hateful of mutants. Anti-mutant bigotry should be an *occasional* plot, not a constant one. Most of the time, fear of mutants should manifest in much lesser manners, like "the family of a student is uncertain how their relationship is changed, on finding out their kid can make things explode with his mind, family drama needs to be resolved".
2. Related to the first one- the MCU is fundamentally an optimistic, heroic setting. When courage and acceptance confronts fear and bigotry, courage and acceptance should win.
3. The X-Men should be superheroes, first and foremost. That means they should be shown doing actual superheroic stuff, in public, not just dealing with "mutant affairs".
4. Roster: I'll be blunt, the 'Original Five' is a terrible idea. It was Claremonte that made the X-Men an actual success, so the roster should largely derive from Claremonte. If I had to pick a roster, I'd take Cyclops, Jean, and Beast from the original, and add Wolverine, Colossus, Storm, and ( if budget allows ) Nightcrawler. Add Kitty as the junior member, though not necessarily at the very beginning. This way, you have a good mix of personalities, relationships, powers, and visuals.
5. Magneto works best as a sympathetic antagonist or anti-hero. Exploit that. Use him primarily as a foil for Xavier, that the X-Men interact with primarily *outside* battle. Have him lead an opposed ideological faction that operates on a level somewhat above "supervillain team". Perhaps he advocates separatism, with mutants forming their own distinct communities. Perhaps he spends a lot of time waging one-man wars outside the western world, against various oppressive regimes whose treatment of mutants is overtly tyrannical/genocidal. Whatever you do, keep him from stepping over the moral even horizon; even if the X-Men do come to blows with him, it should be over grounds wherein he can be understandably wrong, rather than kitten-kickingly evil.