I'm wondering it this will all hinge on May not killing Katya. As far as we've seen, that's the earliest regret to be changed. If May doesn't kill Katya, she doesn't retire as a field agent. This possibly affects who Fury chooses to oversee Coulson since it was revealed that May's personality changed after this event. If May isn't picked to watch Coulson, Fitz and Simmons are never recruited to be part of his team since it was later revealed that May steered Coulson's choices. (Grant likely still is since Garrett was using him to find out about Coulson's resurrection.) This frees Fitz up to go down whatever road he's on, but it has no effect on Daisy becoming an agent since it was Grant and Coulson that found her. And, if Grant finds her without Coulson's involvement or finds her and Coulson leaves SHIELD, it obviously make her a lot easier to flip. Not having May around could also be what leads to Coulson leaving SHIELD, whether it's because he needs her support or because the agent that takes her place in overseeing him has him pulled.
It would also explain why Coulson is teaching about fearing the Inhumans (forgot about that part). Katya is an extremely powerful and mentally unstable Inhuman, which is why May kills her. Having her alive allows her to become even more powerful, and she obviously would have reason to have a grudge against SHIELD, potentially aiding in their downfall whether working with Hydra indirectly or not. And this could lead to Jiayang and Afterlife coming into play.