In all my understanding of balancing content in the game, it has less to do with making particular strong cards weaker, but making them weaker comparatively. You don't need to nerf Hourglasses or Quantam Towers if you can make alternative cards that are just as capable or slightly more useful. Like, instead of using Hourglasses to draw, I could have a water creature that let's me draw a card with water quanta. I completely new way of playing and mitigates the effective "rarity" of card drawing only being in the Time element.
I pretty much agree with what Essence and the others have said. It is not about nerfing particular cards or strengthening particular ones, but to increase synergy inside the own unique Element. For example, with the exception of Ball Lightning, how does Fractal synergise with Aether? Light as an element will have greater synergy now that Light Nymph and RoL work well with Hope. The nature of some cards (FFQ, Sundials, Pulverizer, etc) means you need 2 elements to use it effectively. The Rainbow deck capitalises on the fact that 2 or more elements are needed to utilise the cards that synergise the strongest. Nerfing any of the standard requirements of the rainbow will see some of us using the Nmphomania deck or mono-aether.
In effect, the best way to reduce the usage of particular cards is to let different cards be used in the same effect. Of course, much of your problem as a developer, zanz, is that you need to balance the level of high and low content. While many of us are farming False Gods day in and day out, you still have to cater to those who are starting the game or are still on AI3. IMHO, it should be fairly noted that balancing is not about making cards stronger or weaker, but making them perceivedly stronger or weaker against other cards.