How differently do you think the show would’ve gone if Dante and his little sister Shadow (Denise) were in it?
(Keep the shadow fan series in mind because it details them quite well, and Shadows off and good days between hospital surgeries and appointments)
Note: There is a lot of information in the fan season, so I don't think I can discuss everything.
I think the Mysticons would react differently to Shadow's Health needs. Piper and Em would still fully accept Shadow as a Mysticon right away, but Arkayna and Zarya would be unsure. It wouldn't be out of judgment, but rather out of concern. Being a Mysticon is physically demanding, and they wouldn't want Mysticon business to make Shadow worse. However, eventually, they would fully accept Shadow as a Mysticon. Even at the start, all of the Mysticons would care about Shadow, helping her with anything she needs and being understanding about surgeries and appointments. For example, you mentioned in part 11 that Shadow needs light foods for a few days after surgery. The Mysticons will keep that in mind, ensuring that there is food that Shadow can have after surgery in the stronghold.
You introduced Dante, Shadow's brother. I think he would play an interesting role. He would worry about Shadow being a Mysticon, as just like Arkayna and Zarya, he would worry about it being too much for her. Seeing Shadow with the Mysticons would be an adjustment to. He is used to having to care so much about Shadow, so while he'd be happy that other people care to, there might be a bit of an adjustment with not being the only one caring for Shadow. It can be especially true with Arkayna and Em, as I think they would take more of the lead in taking care of Shadow (between the Mysticons). However, he would end up becoming friends with the Mysticons, and being available for them if they need it, even without Shadow. You also mentioned that Dante often goes with Shadow when she hangs out with the Mysticons in case she needs to take her to the doctor (part 9). I think he would at the start, and while he would continue to spend time with her, he would accept the Mysticons being with Shadow without him, provided all the Mysticons have his phone number and know what symptoms to look for. This idea is further supported in your story, as in part 14, Dante isn't there when they go out for slush gulpies.
Another thing you mentioned is that Shadow stays at the Academy and takes classes there, as mentioned in part 13. This is interesting, as Dante goes to the Academy to, and might want Shadow to stay there when not at the hospital. However, you also mentioned Shadow spending nights at the stronghold. I have a feeling that as Shadow's condition and Dante's trust in the Mysticons improves, Shadow will stay at the Stronghold more and more. There would be a room in the stronghold for her.
Another thing you mentioned in part 8 is Shadow's illness improving. This is important, as how bad the illness is would dictate her role in the series. If her illness is bad, she may have to spend more time resting and/or in the hospital. Because of this, the four main Mysticons will handle a lot of the missions. As her condition improves, she joins in on more training and missions.
They would also ensure that she has mounts once she's well enough to participate in missions. The griffin would come from the royal stables, while the dragon would come from a visit with the Dragons of Light.
Villains, like Captain Kaos (you mentioned him in the fan season, so that's why I'm specifically mentioning him here) would use Shadow's illness against her. Because of this, the Mysticons would be careful with saying anything around villains that could be used against Shadow.