Writers tend not to understand what characters like Superman are - a case study in the idea that "Power Reveals." You want to know who someone truly is? Give them enough power that they no longer have to deal with consequences. Most will show their inner darkness, but a few will suddenly be freed from the idea that no good deed goes unpunished - Superman, Captain America, and other paragon characters fit this bill. Jean Grey should fit in here - I always felt that the Dark Phoenix story involved not only the outside influence of the Phoenix, but the force being corrupted by outside influence as well. Jean sacrificed herself to stop what it was becoming - and claims that she and the Phoenix are one and the same remove her from that nigh-incorruptible paragon that she is at her core. There's a reason why she is the best one to contain such power.
Dark does not mean deep.
In terms of misogyny, Oh, you're not wrong, but it's really old news and I think bringing this up, intentionally or no, is just to inflict some bad-faith feminist outrage. Supposedly giving Jean and Ororo solos solves this conundrum in the reboot, or having the cosmic/astral plane-y threats we do in Fall of X (Orchis is mostly an afterthought to all the sinister/phoenix/Moira stuff).
It's also why the modern trend of bashing Claremont irritates me, because beyond the story themselves he set the groundwork for so much of the social inclusion element in X-men, and pop culture in general, to the point it'd be equally valid to use x-men as a critique of yas queen social domination/overcompensation for the past's assholery, only dooming the cycle to repeat.
As to power levels in general, I thought Excalibur handled this well enough -- including at the end having Rachel set some self-imposed limits totally in character -- but in a large team book, the power arms race gets very boring to read about or forces the scale of the story to change so powerful characters aren't getting Spectre'd (as in a major DC crossover happens, and the spectre prevents it from being an insta-kill for the universe but leaves everyone else to have something to do for the story proper)