Well, there's the fact that June Egbert was the direction Hussie wanted to take the character in before the toblerone wish and that's been said quite a few times so I think it is a bit weird to worry that her transition would just be a joke imo

While I also have some problems with HS2, I really think that the conversation in Chapter 16, about how John felt the need to be the man his father wanted him to be, and how doing that, living in his old house, felt like a prison sentence, and the house being blown up felt like a huge relief, that conversation was really good. The new team I think has been building on it, not necessarily "correcting mischaracterization", tho I agree that that would be the case with, say, Candy Jade, Rose, and Kanaya.

In general, as a trans woman, I've found John's depression and self-isolation, and the way that he just doesn't feel quite "right" as himself, to be very relatable as early as the epilogues. I think some people forget that it was largely the way John was written in the epilogues that kicked off the whole June Egbert headcanon trend on twitter in the first place.

As for specifics on the way I think the story may go, I think that John saw a version of herself from looking into the Hope radiating from Jake(at least, that's what I took away from that one gif), so that seems to have laid some seeds that will probably come to fruition over the course of the long journey to Deltritus, however they end up doing that. Vriska will also likely be involved given her smile flashing at the end of that gif.

In Meat, I feel that John will probably get prototyped with something weird and we'll see her transition like, in the way Davepeta did, basically. Very likely a bunny of some sort, given that line Rose has near the end of OG Homestuck about how there was Dog Jade, Bird Dave, and Cat Rose, but no animal fusion with John.