Now that we can decide when to use runes, I think it would be a good idea to be able to choose whether to use that charge to activate the rune or enhance the cast of an ability, even activating additional effects on the abilities.
The selection and installation of the additional effect could be done from the covenant selection screen. Once the covenant is selected, a screen would appear where each ability and its small list of effects to add to it would be selected.
Perhaps, in the future, they could add a system of additional effects (selectable by the player) for each ability of each covenant. The player would decide beforehand which effect they want for each ability (crowd control, life absorption, limited invisibility, elemental infusion, etc.).
Activation would be as simple as holding down the button or key for the ability; upon releasing the button, the ability would be executed with the additional effect that was "installed" on the ability consuming the rune's charge.