There is nothing wrong with quantum towers, nor with Rainbow decks.
The fact that a fully upgraded rainbow deck can beat a god 66% of the time for me is absolute proof of how well designed the false god's difficulty is. This is very different from the triviality of level 3 AI. A regular rainbow deck with no upgrades suffers A LOT against god, and the journey to fully upgrade your deck is quite long, the learning curve is steep AND learning to play with the rainbow is not trivial, actually it is quite difficult, full of nuances that could lose you the game. I think this sort of game balance is fine right now.
Unfortunately, what is really wrong is that only 2 decks are known to be able to reach such performance, and those are Rainbow decks and mono-aether, and mono-Aether does with without any of the charm. Quantum Towers and Phase Shields allow this to work, and the decks powered by them are not overpowered against other human decks, in fact they have SEVERAL weaknesses! Their real advantage is against false gods which currently represent the easiest way to farm upgrades.
All other mono-decks need a serious upgrade so they can provide the same level of gameplay, and/or the game needs another system to allow players of other decks to more easily upgrade their cards, otherwise they will always be forced into those same 2 decks.