I've been giving some thought to pixie dust. It's a gating item for a lot of things, yet it depends on a pretty rare resource, the stardust plant. (Or moonstone if you're desperate.) It's probably outside the scope of this mod - just fixing things like exactly what you noted there - but what's your opinion on making pixie easier to produce or even removing it as a step in some recipes?
Maybe make it so that those excess Skillbooks that you find can be transformed into Pixie Dust somehow? You could toss them into the Elemental Forge or something.