It’s really difficult to speculate on the full trajectory of Jon’s story if he’d been a girl; the one part that I can apply the change with any level of certainty is girl!Jon’s childhood in Winterfell. Certainly, Catelyn would always resent any bastard of Ned’s that gets installed in Winterfell and given the same treatment as her own trueborn children, but there would be very little chance for a girl!Jon (let’s call her Jo) to ever pose any dynastic threat to Catelyn’s line. Meaning that Catelyn’s early days in Winterfell would not be haunted by the thought that there is even the slightest possibility that Ned might prefer the Stark-looking bastard son that he clearly loved so well to be his heir over her own Tully-looking Robb like in OTL, neither would she continuously fear that her husband’s bastard could challenge her children’s claim and press his own claim to Winterfell against her own children – because while an acknowledged male bastard who takes after his father and is clearly favored by him could manage to gain support for his legally weak claim, virtually no lord in Westeros would ever back the claim of a bastard girl against her trueborn brothers.
Though that does not mean Catelyn would be any warmer to Jo, she probably would not try to systematically push her out of Winterfell as insistently as she had her male counterpart. Her resentment of Jo’s Stark looks might also get tempered to an extent by Arya’s birth, as opposed to OTL where Catelyn continued to resent that none of her sons favored their father and wished so bad to give Ned a son that looked like him. On the downside, Jo would not be able to avoid Catelyn as much as her male counterpart was able to; her gender would put her under Catelyn’s direct control so to speak since Catelyn was the one responsible of supervise the education of the girls. This, I’d imagine, would allow Catelyn to restrict Jo’s education in the feminine arts because no way is she giving Jo an identical education to her trueborn sisters the way Jon received an education on par with Robb’s in OTL. Catelyn’s control of that part of the household would also allow her to emphasize Jo’s status and her trueborn sisters’ superiority to her pretty much all the time.
It’s unknown what plans Ned might have for Jo’s future in this scenario. At 14, Jo would be old enough for a girl for Ned to start having some concrete plans for her, since marriage is the obvious option for her considering how limited the options for bastard girls are in Westeros. So Ned probably would have attempted to make her a good match to secure her future, though the degree of success is speculative and dependent on several unknown factors. At age 14, Jo would not be too young for a betrothal like Ned felt Sansa was in OTL, and while bastards are at an automatic disadvantage in marriage (and Jo would be at even more disadvantage than canon Jon whose gender could have afforded him a nice political standing by Robb’s side, significantly improving his marriage prospects), the example of Alayne Stone shows that their marital prospects can expand significantly under the right circumstances and given the right incentive. Now, Jo would not be without attractive qualities: raised as a Stark in all but name; known as a favored daughter of the Lord of Winterfell who loved her enough to commit a major social faux pas for her; possessing of Lyanna’s wild beauty, Jo could be a nice match for a third or a fourth son, or a minor noble that wants an in with Ned. A Stark, even a bastard Stark, is nothing to frown at after all, and with Ned almost certainly willing to provide a dowry, Jo’s prospects could be relatively good.
Beyond that general idea of Jo’s future, I simply can not begin to speculate how her story’s trajectory changes because the butterfly effects are endless. it starts from the very first chapter of the series: it was Jon Snow who convinced Ned to let the Starklings keep the direwolves after he already refused Robb and Bran in OTL. If Jon is born a girl, his female counterpart would not be present for Gared’s execution, and thus would not be there to make a plea for the direwolves’ lives: where does that leave Arya when Joffrey draws steel on her without Nymeria to protect her from his manic rage? Where does that leave Catelyn and Bran without Summer to kill Joffrey’s assassin? What happens between Ned and Robert if (when) Joffrey hurts Arya? What happens to the War for the Dawn without Bran? It’s not only Jon’s story that would be hard to follow in light of that change, the entire narrative would change and we would be talking about a drastically different story.








