There is not an essential rule/order for every deck, it depends on the the deck.
For example, if you are going to use RoL/Hope you should upgrade 6 RoL first, because Photon/Hope is an epic fail.
If you want to grind FGs, pick one good farmer deck and start upgrading it, usually every post about FG farmer decks include their upgrade order.
If you want to go with your own made deck(s), then I would start upgrading versatile cards. ie. cards that are used among many decks. Some good examples are 6 Supernovas and about 5-7 Quantum Towers. Or cards that improve alot with the upgrading, eg. Electrum Hourglass.