Only the level 100 purple essences (Major Essence) can be used in the crafting recipes for the upgrade to a teal or crit orange (Supreme Essence).

I agree that the Minor and lower level Major Essences need an upgrade path. I suggest a barter NPC that takes 5 (or so) of a type of essence to make one of the next level.

If you are having problems with stacking, check the i-level to make sure it's the same.