The main issue is that while the current Lily system is quite successful, that's on the level of taking something terrible and making it less than good. It's an improvement, but we're still in the negatives.
The two big issues with the lily system is that you only get one lily every 30 seconds, if you want to use a lily for movement, you need either a blood lily up, or someone hurt to heal, and the system's pretty much useless if you're on a big movement mechanic that lasts more than one or two GCDs. This last one especially happens quite often, though the other two is only a little bit less common of an issue.
It wouldn't be so bad if you could just generate blood lilies through some alternative means, like an instant cast GCD "quick prayer" that simply gives you a third of a blood lily or something.
