What if we made balance changes so [unit type] can't be countered by [insert a currently-valid strategy to counter that unit type] ?
In general: that unit type becomes more powerful and players will be more reliant on the other strategies to counter it.
Because there are fewer viable counter-strategies, players have fewer options, which means the game becomes less complicated. But not necessarily in a good way.
In this case, the only way to stop air experimental spam would be spamming SAMs, cruisers, or T3 mobile AA. None of those have good mobility so you'd have to invest a lot to protect any particular place.
Nukes could be used to kill forward anti-air, which would allow the air experimentals to get in and wreck everything, unless you defend the nukes with SMDs. But SMDs can be sniped.
So the game would be all about creeping SAMs and SMDs and trying to protect your creep. That kind of gameplay might be attractive to turtle players, but the rest of us would prefer things to stay the way they are.