Over chat, Kraze gave me a great idea.
He put that since this game is called elements, it should promote ever individual type, but instead it does so with rainbow decks. To fix this, he suggested that mono decks should get 2 quantum per turn. To make it more conditional, how about having it so that it can tell if you're mono IF your mark is the color of your pillar/towers, and if it is, the pillars/towers produce 2 per turn. Now rainbow decks could probably take advantage of this too, but I think this would give mono decks a headstart :]
Edit: Though this would probably give newbies an easier start.