While playing against the top 50 decks I have noticed that the vast majority are Rainbow. To be fair, there are also a fair number of mono-Aether decks, mono-Darkness decks, some Firefly Queen decks and a few rare others doing something different. But the rest are Rainbow. I blame it on Quantum Towers.
Because Quantum Towers give so much quanta, it's easy to just pick and choose the best cards available from any element you like. The different elements have their own strengths and weaknesses, so what is the weakness of going Rainbow? Whatever it is, I don't think that it's enough of a setback to be balanced with the extraordinary amount of flexibility gained by having easy access to every element, and this is reflected with crystal clarity when you go up against the top 50 decks.
How to balance it? I'm not sure, because while in my opinion 3 quanta per turn is too much (and for towers, an extra 3 when they come into play? Ridiculous!), 2 might be too weak. Perhaps instead of nerfing Quantum Towers, a new source of quanta could be introduced that randomly produces one of two types of quanta each turn. Perhaps playing an Eternal Mountain could produce 1 Time or 1 Earth quanta each turn, for example. Having these for every possible combination would probably be too much, but for elements that already work together, it would be a good way to encourage dual-element decks so we're not stuck playing against the same thing.