It was already mentioned, but first and foremost, before anything, we need a better way to generate lilies. No other job's guage is counterproductive to the way the job should play, and no matter how much SE wants to push it, a pure healer will simply never be a thing in this game so long as content is designed for all healers to heal it equally. So first they need to move away from this idea of your guage being effected by Cure/II. Change it to regens or even Stones as using elemental attacks is still part of a WHM.
As for what they can do, personally I think Plenary Indulgence is fine. It's duration is way too short though, 15 seconds just like Divine Bension would make more sense. I also think it should reduce enmity while stacks are up, to solve WHMs enmity issues.
As for lilies. Well, I had this idea in my head that two separate types of lilies could be generated. One from healing spells and another set from DPS spells.
The healing lilies could perhaps effect healing potency of your Ogcds which would really fufill that "big healer" identity, while the lilies gained from DPS strengthens your dps spells.
The idea would be to powerup your heals with healing lilies and power up your DPS with DPS lilies (perhaps they could give us a ogcd DPS ability at this point). Using Assize would be the only thing that costs lilies and it would both benefit from healing and DPS lilies. Lilies would no longer reduce CDs and instead we would rely on the trait, secret of the lilies II (which is hopefully more useful at this point >.>) for CD reduction.
It's nothing solid and pretty basic use for the Lily system, but the main draw away is that lilies both need to be generated easier and be more useful than CD reduction.