Right now in a game when you see or, and probably when you don't you'll throw up a few SAMs, which is good against lvl1, nothing wrong with that.
But if someone went lvl2 air you used to have the ability to attack in early and mid lvl2 using gunships. You could cover your losses by spreading missile towers and other lvl1 defenses around but they wouldn't totally stop em until you get some lvl2 aa. Right now they just get raped by those couple of SAMs and missile towers, unless they didn't build any of course

Bombers are still great but you don't have the build power and res to really get them going when you just get lvl2, it'd probably be a lot easier to get the resources for that if you go lvl2 vehicles or kbots instead because of the builders.
So lvl2 air is still a useful tool to have but one of the ways to use them got removed with the gunships antimissile damage reduction, and that's a shame because it just makes it easy when someone on the other team goes lvl2 air 1st because he'll be such a gimp instead of someone who can really help his team.
There might not be a problem if everyone just uses lvl2 air as an extra but I think it just removes options from the game.
And having missile towers attack ground would just be annoying imo, you'd just get a small xta effect because to be effective against air the aa units need to have quite some range which messes up the balance it would have vs ground units until it just becomes a really weak annoying artillery unit.