Ok so I agree that doubling the Quantum towers is not a good thing. Think Rainbow but twice as fast.
The idea iks sound and I like the way it only stacks with the upgrade thus negating the multiple of these in play. Although I think doubling is where you are going to get caught up.
Like this:
Quantum Tower Base 3x Random Quanta
Quantum Flux Generator (x2) = 6x Random Quanta
Quantum Flux Capacitor (x2) = 12x Random Quanta.
Do you see my point?
I know it expires after 4 turns and that is good but during that time you get 48 Quanta instead of 12 which is a vast gain. Also as it expires when it is stolen what is the effect, I assume it does not reset.
So in short I would say you should make it a plus 1 Quanta gain (Mark Pillars become 2 Quantum and Quantum Pillars become 4) and then when you synergise you still only get (Mark Pillars 3 Quanta and Quantum Pillars 5)
But that is just my thoughts on it. After all it is your card but the balance is tough to get with something like this.
Keep it up though.
Thanks
Scyther