For those that don't know, after you start winning against the Fake Gods with the above Rainbow deck, or something similar, you should upgrade specific cards in a specific order.
Hourglasses FIRST. They are, hands down, the MOST useful card in the deck, and you will NEED them upgraded to improve your win percentage almost imediately.
Otyoughs are next after the Hourglasses. Upgraded Oys cost one more, but they are 0/5 instead of 0/3, which means that they can eat plenty more creatures without being buffed.
Quantum Pillars and Novas are last, after the Otys. I, personally, would upgrade all my Pillars first, before upgrading Novas, because Upgraded Novas (aka Supernovas) require two Entropy Quantum to play, unlike Nova, which doesn't have a cost.
EDIT: Mind Flayer is another good card to upgrade. The cost will increase by one (it's the only Water spell in the deck, so this won't matter most of the time), but it will change from a 2/2 to a 3/4 which makes it slightly harder to kill, and that extra one damage helps a bit, too, on occasion.
Afterwords, you can upgrade to your liking. If you run a Fallen Elf, you may want to consider leaving it UNupgraded, as it can be used more offensively that way, with either killing a creature out-right, or turning it into an abomination, which can be eaten pretty easily by an Oty. Otherwise. However, upgrading it means that you can mutate your Fireflies or Skeletons into strong mutants all the time, but then it's a tad harder to use offensively against the Gods. It's your choice, really.