Might be a little drastic, so see it as food for thought, but how important is the double-jump? Have you tried playing around without it? Or perhaps it could share "ammo" like shots?
I used to have one by default in my own platformers... then I ran into level design issues, like you, and removed it. It resulted in less extra height to skip stuff, and I feel it also led to having to put more thought into every jump when playing. Then again, it wasn't the solution for everything~ :/
Can't those Crystie guys remain as the easy, early game fodder enemy type? Or did that role get taken over by another enemy? Perhaps there could be some "evolved" form for later levels/harder difficulties?