Lilly may contain one L too many for some people, though enough parents are choosing this secondary spelling of a name that's become wildly popular in all its variations to boost Lilly almost into the Top 100. And the Lilly spelling does feel a bit less wispy, a bit more like a name as opposed to a mere flower, than the slender and delicate Lily. Lilly suggests the long form Lillian, but it doesn't need to be an abbreviation for anything; Lilly can stand on its own.
However, if you love the flower name but want to make it a little different, you've got to move far beyond Lilly -- or Lillian, Liliane and sisters. You might consider Susannah, which means lily, or a more exotic bloom like Azalea or Lotus.