Here's what I'd like to see done with lilies:
1) Have them proc from more skills.
As is, the lilies incentivize the use of very little of WHMs toolkit, so having them proc from more skills would let people heal in their preferred way and still get lilies.
2) Have current OGCD skills not use them and instead tie them to a new ability. This is where the system runs into issues as it is now. As a healer, one of your goals is to save mana, and one of the main methods of doing that is using your OGCDs instead of your spells. The issue is that if you want to stack lilies you can't use OGCDs because they'll use them up, so you end up in a situation where you're delaying using skills so that you can shave time off of those skills recast, which doesn't make sense.
As far as the type of skill I think would work well with lilies, I'd personally love something like this:
Ability: Divine Seal
Cost: 3 lilies
Recast time: 15s
Effect: The next spell cast will have an MP cost of 0, a cast time of 0s, and its potency will be doubled. In the case of raise, the target will be raised without weakness.