On the actual topic of flares:
Basically, I would have really pushed for it if I could. I was (IIRC) the one on the balance team to push for replacing spec ops flares with a recon plane, and one of the earlier people in this community to push for it. Unfortunately, said change was considered out of scope for previous patches.
Coming into this patch, it really came down to one question: Can you really see anyone picking spec ops after the command panther changes? The answer, to me, is a resounding no. In fact, infil nades were supposed to go to 25 munitions (not just 20), but even that was rethought given the other changes spec ops was receiving. As far as I and most people on the balance team can tell, spec ops will probably be a competitively dead doctrine after this and nerfing it further (by replacing spec ops flares with a recon plane) would just make things worse. It's an anti-fun ability that never deserved to be in the game, but nerfing the doctrine more would just be a little too much.
Maybe the flares could be replaced, other abilities could be buffed, and bundles could be created, but that's pushing towards a full redesign and the patch is pretty large as is. I wouldn't even know where to start with a redesign, personally.
And yet overwatch flares and spotting scopes were nerfed and while both were bullshit they are clearly tier lower than SpecOP flares.
Also what is the scope for this patch? It changed mainline infantry, support weapons, doctrinal abilities and make up of doctrines as well as heavy tanks, its kinda shifty to call flares out-of-scope.
As for SpecOP's viability - it was not picked for techless heavy in larger team games, it was picked for infiltration nades and command vehicle aura and most of all uncounterable recon on demand, nothing has changed in that regard, it will still get abused just for flares. So how it's okay to nerf sim city but refuse to touch flares, unlike flares simcity was always counterable