I don't have any specific movies in mind, but I'd want the MCU X-Men to be quite serious in tone because of how mutants are discriminated against just for being mutants and show the level of violence they endure as a result, whilst also having those uplifting awesome fight back moments so it's not just all doom and gloom. There shuld be heartbreak and humour mixed in, some horror (Sinister and his experiments would play into that) and hope. It shouldn't be a black and white Mutants=Good/Humans=Bad but be very much a grey area where there are both good and bad humans and mutants respectively on both sides and where an entire group shouldn't be judged on the actions of the few even if it is those actions which is fueling the ant-mutant and anti-human hate for both sides.
When tackling the Mutant hate/racism angle, it should focus on the hated because they're a mutant no matter what the colour (it doesn't matter if you're black, white or blue you're hated just the same because you're a mutant) rather than a specific race/colour thing. However they could have an example where a character is discriminated against and the audience is led to believe it is because they're a mutant and it just turns out to be old fashioned racism just to highlight the similarity between the two.