Inspired by some neat ideas from others;
What if Dr. Strange coordinated the arcane defenses of mages the world over, and people like Helstrom, Jennifer Kale, Voodoo, the Scarlet Witch, Agatha Harkness, Jimaine Szardos, Ilyanna, Shaman, etc. all reported to him, at some level, while lower tier 'monster-hunter' agents like Blade, Ghost Rider, Morbius, Man-Thing and Elsa Bloodstone covered the ground beat? The whole magical community, working together, with some outliers and ne'er-do-wells (like Mordo and Modred and Salem's Seven and Chondu the Mystic and the Enchantress and Margali Szardos and Dr. Doom) gumming up the works.
A Sorcerer Supreme who *actually does something* and doesn't just sit around in his Sanctum waiting for bad stuff to happen, and then trying to play catch-up and deal with it all by himself, after the fact. That would be kinda neat.
What if one or more of the FF had been those 'pure' strain humans, mentioned in Days of Future Past, who did not have the latent X-gene or potential for mutation, and who, upon being exposed to massive doses of cosmic radiation, just got radiation sickness and died over three agonizing days? Depending on which of them were 'pure' and which were 'latent' carriers of the Celestial genetic tweak, it would change things significantly. Johnny and Sue might have been 'pure,' and only Ben and Reed survive (with powers). Or vice versa, with only Johnny and Sue surviving, or Johnny, Sue and Ben. (I'd expect Johnny and Sue to either live or die as a pair, since they are the most likely to share some genes, although it's not guaranteed, since they aren't identical twins or anything.) Johnny and Sue as sole survivors (the Terrific Two?) seem likely to be a far more somber and serious duo, in the wake of such a tragedy, and even a 'Terrific Three' of Ben, Sue and Johnny would be very different without Reed to be there with his gadgets and unstable molecules and endless money-generating patents-for-stuff-you'll-never-hear-of.
What if examination of the blueprints of the rocket, and even some pre-flight photos of the old cockpit, showed a fifth seat, and further investigation indicated that the cabin was stocked with gear and supplies balanced for a *five* person crew, but nobody remembers a fifth person, and no fifth person is mentioned in any text, or shown in any photographs of the event...
That would be a neat one, because Rogue would be a very different character if she had to use her own actual mutant power every day, rather than some borrowed alien wannabe-Superman powerset. She'd likely gain far more control, far faster, since she'd be exercising the ability in the usual rigorous X-Men daily training sessions, both the ability to control when she absorbs powers, and dealing with the absorbed memories, and adapting to the new and varied powersets (some of which, like telepathy or weather control, take a little getting used to!). She'd have to learn to be a *lot* more nimble, to weave her way into combat and get a hand on someone, not being able to trust to her borrowed Kree invulnerability or flight to get her safely into hand to hand range, and not having super-strength to make her blows superhumanly potent (fortunately, her touch is enough to knock out anyone short of Loki!).
I really like the idea of various characters having to learn to make more effective use of their own powers. Rogue's not the only one, coasting on borrowed power, and not being as strongly motivated to really develop her own actual mutant power. I see Blink doing amazing stuff with teleportation portals and wonder why Ilyanna never does stuff like this, and then remember that she's always whipping out her soul-sword and charging into the fray, using her actual mutant power as just a way to get to the fray, and then promptly ignoring *her actual super-power* once it all goes down.
So, in addition to Rogue not gaining the powers of Ms. Marvel, What if Ilyanna never became a demon sorceress of Limbo, and was just a (badass!) mutant teleporter?