I don't agree with changing the targeting priority. I think using spam (not just scouts) to counter high damage, low ROF units is legit. There is nothing stopping you from doing the same. And anything that encourages mixed unit comp in this game should be given a thumbs up.
If your opponent masses a huge army of ANYTHING that is going to counter you hard, and you don't see it coming, you deserve to die. Intelligence is important. But if you see that they are scout spamming, and you still can't defend yourself from it, then you have a real issue. I haven't been the victim of heinous scout spam, but surely gators, flashes, pyros, zippers, razorbacks and karganeth can mutilate them, right?
If it's not just an issue of people not knowing how to deal with it, then perhaps a buff is needed. If I'm not mistaken, the tactic isn't to kill your standing forces, but get to your base. In which case, turrets would be an appropriate counter. SURELY beam turrets and double LLT's are good enough to stop them? If the game is so late that they are massing scouts in these numbers, you should be able to smack down a wall of 10 beamers in no time.
If all that fails, maybe a T2 anti-spam turret would be kinda cool? Cheap, Low dps but fairly high range and extreme ROF or AOE. Something like a long range beam turret or Immolator (if any of you remember that thing

). Even the idea that such a turret exists would deter players from attempting this strategy, if your qualm is with the effect the spam has on fps regardless of effectiveness.
I don't think weird changes to units, MM(?), AA (??) and unit resistances are necessary.