I would upgrade first:
- Cards which have a different effect, when upgraded,
- Upgrades which allow you to use a card in more decks,
- Cards which have a big improvement, when upgraded.
My favorites:
Flying Weapon: You can make decks with flying weapons in every mono/duo deck.
Otyugh: Big change of HP, you can eat more creatures
Fallen Elf: Big improvement of the mutations. Useful in a FG Rainbow deck.
Hourglass: Big improvement.
Nova: More quanta, useful in a FG rainbow
Shards: Only useful when upgraded, shards improve your winning chances in many decks, I often use them.
Sundial: No time quanta needed, you can use it in every deck, if you want.
Photons: Light deck with Hope
Plate armor: Big improvement, but you need a good deck to use it. Rainbow decks use quintessence, so they often don´t use this card.
Phoenix: Fire Speed deck
Ice Shield, Jade Shield: The +1 damage blocked can make a big difference, if the enemy attacks with small creatures(e.g Fireflies, Skeletons)
Dissipation Shield: If you want to use it in a rainbow deck, you can´t use the unupgraded version (only litte use)
Purify: Big improvement of the card, but nobody uses it.
Pillars: many people upgrade them, to make their deck completely upgraded. Advantage: you can use the upgraded Quantum Tower in many decks.