Crystal of Light Delivery Service!

[Rocl]

Off the top of my head;
#1) water - like you said the lv5 MSQ, Oda-san has even told us "don't think too much about it"
#2) fire - defeating Ifrit
#3) thunder - Frixio gifts it to us
#4) earth - defeating Titan
#5) ice - defeating Isgebind, the final boss of Stone Vigil (easy)
#6) wind - defeating Garuda

Frixio was given the Lightning Crystal of Light by Ramuh, so there's a strong primal connection for at least four of them. We seem to forcibly take a Wind Crystal of Light straight from the bosom of Garuda, while I believe we find Fire and Earth after their respective primals dissipate. An attempt to explain the non-primal related Crystals of Light I can only surmise they appear near beings with a tremendous affinity for aether. Another possible explanation is they're all loosely tied to Ascians.

Ascian summons the voidsent you get water from, Ascian wakes up and empowers Isgebind, Ascian teaches the art of summoning Primals, etc.

Aaand source for my Oda-san quote: http://gamerescape.com/2015/06/18/lo...h-fernehalwes/

A: With the Blessing of Light, the Warrior of Light is able to manifest of Crystals of Light. Most are thematically connected to their acquisition, but the water crystal just sort of appears. Is there any reason the water crystal was chosen for that or any kind of connection we can make?

KF: Oda-san just said, “Ehhh, don’t think too deeply about this one.” We can leave it at that. <laughs>