It seems to me that Primals are summoned ex nihilo using pure Aether, while Eikons use an existing object as the medium for summoning; Sephirot was supposedly the first sacred tree, transformed by prayer.

Interestingly, if I'm right about this, it would mean that Shiva, the Knights of the Round and Phoenix are technically Eikons. It also raises some interesting implications regarding Odin/Zantetsuken.