The stratagems system of scholar in FFXI was one of the best systems in that game and I feel like it has a great place with scholar in ffxiv as well. Stratagem charges could very easily replace aetherflow (the whole damn thing) for scholars. It would introduce a sort of system that parallels the cards of arcanist but in a new way. Charges of strategems would achieve goals like spreading future heals/shields/damage, extending or intensifying effects, and so on.

http://ffxiclopedia.wikia.com/wiki/Stratagem

That's the list of stratagems from FFXI for some insight in to what they are and what they can do, but I have always felt that they are a system that is missing from the class in FFXIV, far more class-defining than the fairy and the class "style" that scholar has been shoehorned into as a result of being melded with SMN. I don't mind them having a fairy but I don't have any idea what it has to do with being a scholar.

The system would be something like this:
You can hold up to 4 stratagems at a time (displayed on the new UI as 4 in a cross, something similar to the aetherflow ui is in style would be fine). Each stratagem can be consumed to create an affect that is applied to the next viable spell. Choices include:
Light stratagem: Celerity - Your next healing spell with a cast time becomes instant.
Light stratagem: Penury - Your next healing spell with a cost becomes free.
Light stratagem: Accession - Your next beneficial or healing spell with an effect is applied to targets nearby your primary target.
Light stratagem: Potency - Your next healing spell is cast a second time for free on the same target.

You would have a similar idea for attack magic spells as well, although I feel like the keybinds are getting a bit crazy by then.

You gain one charge per x seconds (15? 20?). You can use as many charges as you want at a time but only one of each effect can be active at a time (the UI would show which charges are on cooldown, and which buff is contained in yet-unused charges).

This is basically a resource system that makes the healer flexible; they can buff spells in whichever way is the most beneficial for the moment. Obviously the effects would need to be balanced against each other and which spells they can be used on and so fourth so there isnt a clear cut winner every time.