Quick note:
There is only one true counter to spells.
Quintessence.
I think that's going to be very important.
That's absurd.
In few scenarios does Quintessence do anything better than merely breaking even. If a player has 6 creatures and 6 quints, while the opponent has 6 CC cards, the quints and CC basically cancel each other out, except that the player with the quints has to spend quanta on them, which isn't even breaking even. One of the very few conceivable ways in which Quintessence counters anything is if your opponent's deck has
more CC than you have creatures and quintessences.
Of course, this isn't even addressing all of the non-CC spells, like Fractal, Poison, and Miracle. They still see a bit of play, don't they? And Quintessence does nothing to help you against them. Let's just say there's a good reason it's almost never used at top level PvP.
So, what actually counters spells? Well, nothing. Which is good, because there are a lot of different spell cards, and a card that countered them all would be OP. Instead you have to take it case-by-case.
By the way, I should mention that decks should be compared to decks, rather than cards compared to cards. For example, the best counter to Miracle depends on which deck Miracle is being used in. If it's used in a SBLAD, you can counter it with a fast Immo, but if it's used in a Firestall, your Immo won't fare so well. Trying to determine which cards counter each other is not a worthwhile pursuit at all; you should try to determine which decks counter each other. If a card cannot possibly be used in a good deck, it's UP, and if a card is crucial in the best deck(s), it's OP.