I think the first RTS that finds a way to punish focus fire will be the first RTS that's actually strategic. I mean, if you ever think about how war is supposed to go, focus fire is simply a myth. You don't see 10 tanks all point their gun at the same tank because that way it kills one tank really fast, because it just doesn't work.
For example, take ROTK 11, which is a turn-based game so you'd think the usual surround & kill strategy works even better since there is no time limit, but the game actively punishes the surround & kill strategy if you don't think about it. Let's say you're up against Zhang Liao's unit, who possess the special ability Majesty, which is possibly the nastiest special in the game (unit who get hit by it basically cannot use their specials). So you surround him and try to kill him, but when it's his turn he'll use Cyclone tactics, which hits every unit in melee range and inflicting the Majesty effect. Now most of your army has their specials disabled and is basically just a sitting duck and the opponent only has lost one unit (granted it's one very powerful unit). If you're smart you'd immediately retreat behind your fortification and hope that will buy you enough time for you to get your specials back as opposed to continue fighting for certain doom.
Also, all units in the game can use explosive traps, which is basically a large AE effect that must be targetted on one of your own unit (and it hammers that unit very hard) and hits all units in range indiscriminately. If you just blindly surround & kill a unit, that just induces the opponent to explosive trap the dying unit, since it is surrounded mostly by enemy units and about to die anyway, you will most likely come out worse. So a lot of the game is about how to spread your units out and ensure your ZoC denies the enemies of a chance to use an explosive trap that will hit mostly your units, which means you see a lot of 1 vs 1 even when there are 15 units on each side in a battlefield.