Regardless of when they give Magneto his powers, the point still stands that World War 2 ended in 1945 and the MCU is currently in 2023. Even if you have Magneto born at the very end of World War 2, in 2023 he'd be 78.Given that he probably won't appear until a few years down the line, you're looking at an 80+ years old Magneto. If you have him born during world war 2 or even just before, you're looking at a 90+ years old Magneto.
A flashback movie could feature Magneto and Xavier, but present day MCU they are extremely old. Xavier they could get away with being younger (but still middle-aged) and have the friendship between the two men be cross-generational, however because Magneto's history is tied to a real world event and time is marching on, it would be difficult to have him not be an elderly man yet also keep his holocaust backstory. It's kind of got to be a choice between one or the other. Also I don't think they should give slow aging to Magneto just to make him fit because otherwise that takes something away from Wolverine. Wolverine's slow aging is tied into his healing factor. I think there were some mutants in the comics who did age slower than normal (but not to the extent of Wolverine's slow aging) but Magneto wasn't one of them.
This is why I think Polaris might be a good one to use. She is Magneto's daughter and practically has the same powers (so can fulfil whatever role Magneto's powers would be used for), if she was raised by him, she'd have the same ideology so any anti-mutant sentiment would feed into that. She's not featured in any of the previous X-Men movies so she would be less known to the general audience which means there would be more freedom to use her in certain capacities. They can have old Magneto appear and die of old age which establishes the connection between the two characters. I don't think the MCU will have too much focus on Magneto and Xavier on account of the fact the X-Men prequel movies focussed on them and it could be seen as re-treading old ground.
That could work. There could be a few isolated anomaly like cases (eg Wolverine) in the past which were kind of swept under the rug. In present day, with the sudden emergence of mutants post-Snap, blood work could be done which provides evidence of an X-gene being present which was activated due to the Snap. Not everyone who was Snapped has the X-gene (so Spiderman's friends aren't getting powers) and those who do have different powers because everyone's genetic make up is unique to them. It's also discovered that the X-gene is present in people who weren't snapped and that it's dormant but can also be passed on to off-spring (whether the X-Gene is active or not).It would be a good way to introduce Hank McCoy as a doctor studying the X-Gene (which can inevitably lead into him turning into Beast) but wasn't Mister Sinister also some kind of geneticist? If so, it would also be a good way to introduce him. Stark Industries could provide the machines used in the analysis and studies of the X-gene (which keep Pepper and Morgan relevant rather than just being cast aside after Tony's death), maybe even have Jean Grey as McCoy's young research assistant/intern in a minor role which then sows the seeds for the Phoenix saga somewhere down the line. Xavier could maybe be in collaboration with Hank McCoy without being too much of a focus, perhaps funding the study. With Sinister on the scene, we might even get the Morlock massacre. Perhaps Sinister could've experimented on them (they were homeless people so were easy targets) and the massacre is Sinister's way of trying to tie up loose ends. As Nathaniel Essex, he would be highly respected for his work in the field, so he doesn't want any of the Morlocks exposing him.
If I remember rightly (so please correct me if I'm wrong) but I think Gambit and Sabretooth were on the team that committed the massacre. Gambit led them to the Morlocks and was horrified at what was happening so he managed to save Marrow and get her out of there whilst everyone else was slaughtered. Gambit could've been introduced previously as a thief for hire, maybe even being hired by Essex to break into Stark Industries (perhaps to get the blue prints for some technology that Sinister wants to build and use in his experiments) and we can get a cool heist scene. Maybe Sinister even privately hires Justin Hammer to build the actual machine for him (thus bringing Sam Rockwell back to the MCU)
Since Hank's study would need people to provide blood samples, perhaps that is how the X-Men actually meet. Cyclops, Storm and Rogue could all be participants alongside cameos of other mutants. Given that Rogue's powers mean that she could theoretically kill someone just by touching them, it's natural that she would want to find a way to control them (or treat them) so that she's not such a walking murder weapon. This then sows the seeds for her taking Captain Marvel's powers.
As for who could play Sinister, maybe Johnny Depp?
I've changed my mind yet again on the Rogue casting, this time I'm suggesting Adelaide Kane.
As for Sabretooth, I'm tempted to say Liev Schreiber (because he did a great job in X-Men Origins Wolverine, even if the movie itself had its faults).
I'd keep the Hank McCoy, Gambit, Jean and Cyclops castings I listed above.
Storm I might change to Mekia Cox but undecided on that one.
Will have to think of people for Xavier, Magneto and Polaris.