There are a couple of mods that help with the air combat problems, but I've decided to wait for the expansion rather than add a mod. Hopefully the devs will come up with a balanced solution instead of a guess from a third party.
As for the air attack targeting, the naval strikes are completely out of your control, other than to put air units on naval strike priority. Base attacks can be targeted specifically, and you can choose between port attack, airfield attack, and ground forces attack. In addition you can choose the attack altitude for most air strikes, which influences losses from AAA and strike accuracy.
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