I have a feeling, that reason why lilies seem like a weak mechanic is that you dont "see" the benefit very clearly.
But is IS there. If you can use ability like DB/Tetra/Assize with 3 lilies, you will get it back much sooner which can be important on hard encounters.

It is just hard to perceive the benefit on easy fights, where you barely ever need to Cure or use affected abilities on cooldown.

PS: one change I wich was made is getting some low percentage to proc lilies from offensive abilities (stone at least).