There's no neat way to bend the rules just for Flare - you need specific card text on either Counterspell (e.g. "Does not counter Flare") or Flare (e.g. "Immune to Counterspell") to make that happen, which is very inelegant.
Also, it's fair since Flare is only a 2-mana card while Counterspell is a 3-mana card. If you use Flare to trigger Counterspell, you are actually ahead tempo-wise and can safely use other more valuable spells.
So yes, I think Counterspell should counter Flare too.
If you think that flare should still get its effect when counterspell is in play, do you also think other spells should get their effects while counterspell is in play? For example, should deadlyshot kill an enemy before counterspell is triggered? Spells should be treated the same regardless of effect after all, it's not yugioh where you have different spell speeds.
Personally, I feel like Flare should destroy Counterspell, purely based on the flavor and feel of the card. However, if it did work this way, as others have pointed out, it wouldn't make sense based on Counterspell's text and the mechanics of the game. There's no good way to redesign the cards so that Flare does destroy Counterspell, so I guess we just have to put up with the sadness of our Flares being countered. Or use Eater of Secrets in wild.
Hear this out as it would allow things like Flare to work as many of us think it should.
What about instead of Flare being a spell, make it a form of ammo for combat. There are other cards that this would make sense to do with as well. Rogue Poisons for example.
Something like this would still allow counterspell to work properly. Perhaps Deadly Shot, Flare, multi-shot, etc have their mana reduced by 2, but the player has to load their hero power and subsequently use that hero power for it to go off correctly or loaded and saved for use. A similar concept for the Rogue would take some working out, but it could work as a good alternative.
Do I want it to? Yes! It's a flare that exposes everything. Should it? No, because by the logic of the game, a spell is nullified by Counterspell. You can't counter a counter if the secret goes off first. The line of logic in the code doesn't allow for that without exceptions.
Now if they made it a 1-mana 1/1 weapon that had the battlecry or "when attacking" effect of Flare's card text, then absolutely, it makes sense in both flavor and language of the game.
Side note: this is an OLD argument and we gotta stop rehashing in forums that Blizzard doesn't take seriously. Go on Twitter and @ the dev team with ideas on why you thing Flare should beat Counterspell, or why it deserves a rework.
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Rage quitting: the best way to ensure your opponent knows they beat a giant baby.
The only gripe I have with it is the flavor from Wow that interrupts don't work on non-spells. Flare is a spell only because there's no other category it could be included in for HS. Just like many actions in HS that wouldn't technically be a spell in a broader setting. Shield Slam for example, you smacking a guy in the face with your shield, that's not magic.