Umm, what exactly is the problem? The meaning of "healing magic" vs. "healing done" or "healing done by your spells", etc., has been consistent since 2.0.
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Also to add to this SCH does have traits in the form of Maim & Mend I and II, and AST gets a pot boost from whichever sect is active. I know the base potency of the heals is still like you said though, but they do get something.
I think the concern is that with each expac, healers are only going to get even more abilities that are not effected by the likes of Largesse. Of course abilities generally have higher potency to make up for the fact they are not effected by these pot boosts, but perhaps it could be nice to have a skill that effects abilities more in the future (not necessarily a pot boost, maybe like the ASTs old Spear effect that reduced ability recast times temporarily).
I'd prefer it that way, personally. Otherwise Largesse ends up just feeling like Power Surge did -- button bloat that acts only to make your abilities deal their "normal" effect, such that you're badly penalized if it falls out of sync. I have no interest in seeing that in what's supposed to be a precisely timeable and responsive toolkit.
What I'm not okay with is Defiance not affected ability-based healing. That's just a massive, blaring imbalance.
Honestly, no. Let's put it this way: in the dominant spread of pre-Savage of content, buffing anything outside of abilities is largely situational, or at least not "rotational" in the same way healer oGCDs are. And, honestly, that's how I'd prefer to see Mantra, Fey Illumination, and Nature's Minne used. If anything, I want them to be timed to a buffed shield or HoT, never to the alignment of healer oGCDs. As such, they work fine, imo. The only imbalance is that Shield Oath and Grit both affect eHP as restorable by either Abilities or Spells, while Defiance only affects Spells. As content is further and further outgeared, and more abilities added, it falls further behind the other stances.