I've quite a few questions about them and honestly all my research into official threads, item descriptions, and quest text has only provided me with this information

Soul Crystals impart abilities on their carrier

Not everyone resonates with them. I'm assuming this is either done by ones resolve or similer Aether

They can be crafted by those with the knowledge (Machinist gave us this bit of information)]

The knowledge apparently isn't that secretive. Ninja's have soul crystals and they're on a different continent.

Experiences can enhance them

But WHAT are they. I've an idea they're a type of meteria, but how exactly do these little rocks work?