Crystals

[Cilia]

The crystals do seem to be tied to your blessing, as they appear in your mindscape after getting each one and after Middy strips your blessing that mindscape seems to fall apart. Anyway, you get them in order as follows:

Water - Lv5(ish) starting city quest.
Fire - Defeat Ifrit.
Lightning - Rescue Frixio from the Thousand Maws of Toto-Rak.
Earth - Defeat Titan.
Ice - Defeat Isgebind.
Wind - Defeat Garuda(?).

EDIT: Yep, the Wind Crystal is the last one you get, after some kind of feedback from the Echo forces it out of Garuda when she tries to temper you.