So from the welcome back campaign we see the line
"In the dark the crystal waits dreaming"
This says to me that the crystal is in someway conscious. That it is capable of thought.
We also suspect that the Allagan's either did something to Dalamud or altered it in some way. (Cid calls it a satellite I think.)
In one of the concept art photos the text was translated as "Aetheryte that cannot be used, to show that it cannot be used it is red"

Long ago the Allagan empire discovered the power of the Aetheryte, but they could not harness this power because the aetheryte was a conscious living force. Either they had moral misgivings about using it or they simply couldn't. So they extracted the consciousness from the aether (Pulled it's brain out so to speak) and put it on Dalamud, or made Dalamud out of it.

Aetheryte that is alive is red, and can't be used. Dalamud used to be white, because it was either dead or just sleeping / unconsious for a long time after the Allagans split it up. Whenever the Garlean empire began project meteor they woke Dalamud up. They can't control where it lands because Dalamud is alive, and it's in control.

The primals are an unforseen side effect of extracting Dalamud's consciousness. The Allagan empire in the past was capable of defeating them, but due to the devastating effects of the umbral cycles they no longer exist, and an answer to the primals is not readily at hand. The Garleans, upon discovering this, believe that the only solution to stop the primals before they get out of control is to re-unite Dalamud with Eorzea.

My theory probably has quite a few flaws.
If you know of anything in game that directly invalidates it I'd like to know so I can try to revise.