Runecrafting is a pitiful method of generating runes, as a lot of people know already. The introduction of Protean Essence has dinged it even further, by providing a method besides Runespan to train the skill that doesn't make one hate existence. My proposal is that we make a new item; refined essence.
Essentially, it's a stackable rune essence that is used over time instead of all at once. The experience and runes per hour probably should be lower than if someone used traditional runecrafting, but being able to use it passively would make it MUCH less soul crushing than doing those runs for the same amount of time.
Creating it would take two methods; one involves using the Protean essence (and would be basically free from there; don't want to obviate Protean essence right off the bat), and the other involves using various other in-game resources to transmute normal essence into refined essence. Possibly involve one of the lesser used Invention componets?