Time Warp | Time Warp Again {Yay! No need for (upped) tags}
I think I can easily abuse it: Only play 1-2 cards(1-2 time factories) in the first 5-3 turns, then play this to reshuffle all their pillars(and anything they played with the quanta they gained so far). Then play your remaining opening hand pillars. However triple check my evaluation of this one, this kind of effect messes with my intuitions.
Note that that is a trick that would only work once since after the first time, your opponent would start holding a few things back. Also note that if you are employing that strategy, you are passing up the opportunity to damage the opponent while they damage you. One last note: Your quanta is reset, your opponent's is not, so they come out at an advantage for getting cards out faster. Now you might be able to pull off some interesting things by playing this, then playing towers to power out a creature at an empty field, but that takes a lot of effort. So yes, with the right setup this card can be pretty strong, and that's the point.
You are underestimating the power of putting all your opponent's quanta sources (besides their mark), and everything they spent quanta on so far back in their deck. Sure they have some quanta left. However they just had their turn so they are unlikely to have much excess & the game is still early so you can tank the early damage.
Would people start holding back when they saw an opening 1-2 Time Factory play? If they went first then they either already messed up by playing their pillars or they yielded the 1st turn advantage to whatever deck they are facing. Even worse, if they are facing a stall time deck, the stall time deck can do the 1-2 Time Factory play to earn 3-5 free turns of stalling. So unless this single card dominates a large number of the PvP decks, the only counterplay to it is overall harmful to the person using the counterplay.
The submission is creative, but early game destruction(via shuffling back into the deck) of all the opponent's quanta sources was something that made the balancing that much harder.