Skill blooms, especially the Rainbow Skillbloom (500 crystals), but if you don't have a rainbow girl yet, and don't want to stock up on these skillblooms in advance, then gold skillblooms (250 crystals a piece) are a good investment as well. It's easier to raise the skill through skillblooms (guaranteed skill-up), than by merging with a copy of the same girl (harder to obtain, and you're not guaranteed to get a skill-up).

No need to use skill blooms on girls that were event rewards. It's better to use skill blooms on girls you obtained from Gacha.