Daud uses Runes to upgrade Arcane Bond, giving his assassins new powers. Source: DLC supernatural abilities page.
Daud's Whalers have to put some of their own effort in to get better. Source: the Whaler in training during The Flooded District mission.
Delilah gives her witches powers with her version of Arcane Bond. Source: Harvey said it somewhere. Does need a reference though. Any idea where that would be?
Gravehounds are the hardest power to master. Source: overheard conversation between two witches outside the Dunwall Tower waterlock in Death to the Empress. One said they had finally mastered it, the other that only a few ever did and that Delilah would be very pleased. Possibly just my interpretation of it, I suppose there could be other powers that are even harder to learn.
You probably know half of this already, but I thought I'd better write it all down here, so there's no mistake of where I got any of it.