Personally, after I upgraded my hour glasses, the very next thing I did was upgrade my novas. It's extremely powerful. Also a quantum tower is by far more valuable than a nova (so you would never use novas if you were using all quantum towers).
A nova gives you, on average, the quantum you would get from 4 turns with a quantum pillar.
A nova gives you, on average, the quantum you would get from 3 turns with a quantum tower.
A supernova gives you, on average, the quantum you would get from 8 turns with a quantum pillar.
A supernova gives you, on average, the quantum you would get from 7 turns with a quantum tower.
A quantum tower gives you, on average, the quantum you would get from a quantum pillar in 2 turns.
If your towers don't give you 2 lousy entropic quantum, then it's just bad luck. It's clear that supernovas are better than towers when you are starting out.