Franklin Richards has been one of the Marvel Universe's most powerful mutants, since his birth to Susan Storm of the Fantastic Four. Approaching godhood with reality-bending powers, his abilities were suppressed by his father as a young child, though they began to leak out. He created universes as his playthings, and in Secret Wars, remade the multiverse with Molecule Man. Recently, as his powers began to run out, he became an even greater character of interest to the mutant nation of Krakoa, fearful the same could happen to them. The X-Men/Fantastic Four series by Chip Zdarsky investigated that relationship and left Franklin as a mutant ex-pat, living with his family but readily visiting Krakoa and the other mutants. Zdarsky expressly wrote the story as an analogy to a queer or trans experience, telling Precious Baubles that it was like a "queer kid being raised by leftie super well-meaning parents who will always say they understand but don't understand 100% and they have to find their community elsewhere." He also talked about picking up on Dan Slott's revelations in the Fantastic Four that the Richards had, basically, chipped their kids to keep track of them, and revealed that Reed had used that to mask Franklin Richard's mutant identity from Krakoa.
Dana Kinney for Women Write About Comics called it "a story about the closet and the complexity of well-meaning families, posing small but complex questions such as, "how could a family who loves their child ever hurt them?" The series offers a simple but nuanced answer: by refusing to accept who your child is and trying to force them to be something else, one of many struggles that queer & trans readers experience throughout life."
Stephanie Burt for Xavier Files wrote "Franklin worries about power loss. That's narratively required because Chuck needs a non-terrible reason to bring him to Krakoa now, rather than waiting till he turns 18. The power loss doesn't make sense with Jews as mutants– you're not less Jewish when you turn 18– but it makes a ton of sense with mutants as trans kids, since parents who won't allow medical interventions for trans kids who require those things are parents who want those kids to "grow up" to be "normal"… and they can do irreversible damage."
It is worth also noting that there are many depowered mutants living on Krakoa, whose abilities were taken away on M Day and a number of whom have had them restored, directly or through Krakoan rebirth. What Xavier says, however, is that Franklin was never a mutant, and it was all a lie. And has somehow just determined this and told Franklin via a mental text. Despite the X-Men/Fantastic Four series repeatedly confirming his mutant status and wanting Franklin to join them.
Which means when, in Fantastic Four #26, Franklin Richards is revealed by Professor Xavier to never being a mutant, that it was all an illusion caused by the same cosmic powers that fuelled the rest of the Fantastic Four, and he was no longer welcome on Krakoa, it hit some readers harder than it might have otherwise. Franklin used his powers to make other people think he was a mutant, but never was. Which has been interpreted by some as an intentional slam on the trans experience.
Dan Slott tweeted out "Marvel Comics is serialized storytelling. Every issue is a chapter in an ongoing tale. The story is always evolving and building. If characters keep standing on solid ground things get predictable. 'What just happened?!' is what gets readers to 'What's going to happen NEXT?!'"". And in his Marvel 616, he seemed to relish in some of of the vitriol he received for killing off Peter Parker when we all knew that it was a temporary aspect of a much wider story. He followed up saying "Come at me hot on social media and mischaracterize me as a person because you're mad about a comic book? That's a pretty good way to get blocked. Maybe calm down and pretend you're trying to initiate a serious conversation w/ a fellow human being first. That'd be a good start."
However, the trans allegory response may have blindsided him on this one, leading to a little backpedalling as more threads landed. "The X-Men metaphor is tricky because the metaphor means so many different things to so many different groups of people. To some it's race and/or culture. To some it's sexual identity. To others it's just a general sense of feeling different from everyone else… the way I've seen it for Franklin is that being a mutant was giving him a sense of community outside of his family, something that was special and just his– that none of the other Richards had. And now, through no conscious choice of his own, it's something he's lost. We had a talk with the X-Office about the specific language of the page and the situation, and– believe it or not– the dialogue that was there was a compromise that we could all agree on. Thought was put into it, but as is clear with yours and others' responses we could have done much better. And I can promise you that we will strive to do better in the future."
And to other objections, "Please, and I mean this sincerely, I do understand why many people are hurt and upset by that sequence. It was not my intent. And I am listening and taking to heart why this is the source of people's pain, and I will make a concerted effort to take these very real personal concerns into account in the future… I realize what I wrote and how I wrote it was a mistake, that people read it, were justifiably hurt by it, and I have apologized for it the day it the story came out and once I saw that, and I will continue to apologize for it and try to do better about this in the future."
Though the knowledge this was a compromise suggests that a) it was originally more extreme and b) there is another version the X-Men office would have preferred as well. Might there be calls for The Hickman Cut? What will Fantastic Four #27 bring? What happens the next time Chip writes an FF comic? And how does this tie in with Skottie Young writing Strange Academy scenes in which also-now-never-a-mutant Scarlet Witch is invited by Magneto and the Beast to visit Krakoa?