Brad has said that counterspells were inspired by MTG. I think it's worth looking at some characteristics of MTG counters.
(1) In MTG, you can see whether your opponent can counter your spell, and if they cast something big, they can't (because all their mana sources will be tapped out). This is actually somewhat present in FE: if your caster is working on something with a long casting time, they can't cast Counterspell. However, in that case you should probably counter them, and besides, they could have more than one caster.
(2) In MTG, you can't counterspell all the time, since you have to actually have a counterspell in your hand. You could increase your chances of being able to counter, but at the cost of decreasing your chances of doing anything else. I don't see how this could be implemented in FE without a major change to the game mechanics.
(3) As a corollary, in MTG you can run your opponent out of counterspells, or force them to guess which of your spells to counter.
So, I think making counterspells resistable probably makes some sense in FE, it's a game that relies more on randomness (although I know I'll be ticked off the first time someone resists my counter). But it'll still be obnoxious in tactical battles to go up against someone with high spellcraft (or whatever the youcan'tresistmyspells stat is).
Could counterspell be balanced out better by importing some characteristics from MTG?
For instance: what about putting a cooldown on counterspells? So I can counter your Fireball, but if I do, I can't counter whatever you do next. Ideally, make the cooldown visible to the opponent, so they know how long they have.
More drastically, what about putting an "inverse casting time" on counterspells? So instead of the mage waiting two turns, then casting them, they cast it, then have to wait for two turns before getting another action?
(I haven't looked into modding, but I believe that at least a cooldown is just an XML change)