E and BT cost
Forget it. Godde is spot on that it puts a 'barrier to entry' as it were for units, but that only prevents rushing. Rushing gunships isnt a problem- in fact, thats all they can do early game and they are actually pretty weak as a starting factory.
E and BT are a one time upfront lump cost, and after the investment, the more gunships you make the more efficient that initial investment becomes. This only encourages late game massing, precisely the problem we have.
Gunship arc and countering fighters
Gunships used to have a lower firing arc, and they were almost totally useless. Air just made them entirely redundant, they were a glass cannon you used once in that tiny gap between when they are useful mid game and before the enemy has planes. When we increased their firing arc, this made them able to fight back vs fighters, meaning they were not just straight up hard countered by another factory. You are right in identifying that as the change that has put gunships in vogue now, but going back to a smaller arc is just going to bring back the old problem.
Google is right about the dedicated fighter. IMO we should give it the HP buff it has in 1faction. We dont want multirole fighters to trounce gunships, but a dedicated fighter should beat a multirole gunship more easily than it currently does.
Massing effects and AoE
Yog has got it spot on, its lancasters square law, combined with mobility and versatility. Once these guys mass up and get rolling, they can be a bit hard to stop. The solution has been correctly identified: AoE.
So why dont we have more AoE AA?
One problem with AoE is planes. Planes always lump up, often into tight balls, and it can be very hard to get them to not do this. Having an AA weapon take out a whole wing of fighters or an entire bomber wave is frustrating if there is nothing you can really do to control how tightly your planes clump. We should probably add air collisions back in, though this still doesnt help all that much.
You also dont want to be overzealous with the AoE AA. Gunships -need- to stack up in late game, just like any other unit, since you're working with larger resource numbers. If you can only ever use a small force of them, they will get eaten up by the massive swarms of land units anyway (lancasters square law working against them). It would also not be fair for AA to get AoE without also reducing their DPS, which would make them worse vs single targets (say, bombers). So AoE AA needs to be dedicated to the role of softening up large forces, as a conscious reaction to enemies swarming air units, rather than as something you get for free.
Where to put it all is a good question. The answer is easy in 1faction because we have more than enough units and models for this though (Say, bring back AoE flak).
We do have a last-resort AA weapon for when you just need to say 'fuck you' to an air player though, an AoE AA weapon which will tear through any air force, and that is the mercury, which as stated is very good against gunships. Its serious flaw is that gunships also counter it easily, by spamming blastwings and bladewings. Without that fundamental flaw id say there would be much less of a problem.
Ultimately though, gunships are hit by land, so having a dedicated 'anti-gunship' AA is kind of missing the point. It could be very misguided to have a specifically tailored 'anti-gunship' AA (the packo is bad enough!) when ground units hit them too. There are plenty of land units that do quite well vs gunships and even have AoE (including most riots and many raiders). Even most defenses do fairly well against them. You shouldnt actually have to field that much AA vs gunships, if you ensure that you choose a land force capable of hitting them (NOT most assaults). If you mix a few flaks into a good army of banishers and levelers, you shouldnt have much of a problem with gunships and still be able to press with your ground forces.