I can think of a single way I'd change the entire series for the better in this regard; make Ashildr Clara's mistake. Rather than the Doctor use that 'medkit' on her to bring her back to life, have Clara do it behind his back. Have her cross that line, and then in turn have Ashildr be her ultimate undoing, albeit by mistake. As it is, it never really felt like she truly crossed the line, I never had that moment where I was like "she's too far gone, they NEED to be separated" as with Rose - and I use that comparison as Martha, Donna and Amy never really went that way, any of them. Martha never got the chance, Donna was too good to end up that way (but in a sense accidentally overstepped the mark in a different way altogether in absorbing the Doctor's knowledge) and Amy had Rory to keep her grounded.