Of course, as kobisjeruk said, the deck will not work without the supernovas and SoGs.
After that, I'm not sure how much missing an upgrade hurts, so my judgement may be a bit off. But this is what I think the upgrade priority would be, just from playing with the fully upped deck:
Hourglasses: card draw is important, and as you are entropy marked, you need every last time quanta to draw cards and survive early in the game.
Pulverizer: similar to hourglasses; permanent control is vital for most gods and gravity quanta is of high value.
Permafrost: that one extra damage blocked for each creature is significant and will often determine whether you survive.
Antimatter: the earlier you can play it, the less damage you take, and not having to wait two extra turns for the quanta really helps.
Lava Destroyer: if you don't get enough damage, you risk decking out, and two damage is more than it seems. It isn't really just two damage, but two damage for every turn the lava destroyer attacks. Especially important when you fractal destroyers.
Elite Queen: again with the damage; that 1 extra damage is 1 extra damage every turn a firefly attacks for every firefly. Also important when fractaling destroyers. FFQ might even be higher priority than destroyers.
Quintessence: this deck is somewhat aether-heavy, but more importantly, every turn you wait for quanta to cast quint is a turn you aren't using a creature.
Towers: three extra quanta is great I guess. A fast start really depends on the supernovas though, so these aren't as important.
Fractal: one less quanta cost can't hurt. Most of the time you'd have enough anyway though, and you wouldn't save one quanta because it drains it all.
Miracle: the deck really works fine without this. Due to its high cost, you often either aren't able to play it in time or have everything under control already. It can occasionally pull you through a tough spot, but it's uncommon enough that miracle shouldn't be prioritized over any other card. While at least having it in the deck is debatable for the upped version, the unupped's higher cost makes it almost useless. And if it's for EM, it's better to draw another card that immediately helps survival, which you might be struggling more with due to not having a fully upped deck, than to hold a dead card that doesn't even guarantee EM anyway.