Aircraft in cities are vulnerable to enemy bombing, while those on airbases are not. One turn as NATO would show why the aircraft are not pre-placed on cities, as there would be nothing left by the time they got their first move. The airbases in this scenario were placed on a case-by case basis, essentially reducing them to the absolute minimum. I also try to place them close to cities whenever possible to prevent culture swapping at the borders.
I know what you mean about the crazy problems with airbases. I haven't seen the locked allies declare war over it in this scenario, although perhaps others have. The next release will have mutual protection pacts removed as well to reduce these kinds of problems.
Speaking of which, the next version is a big improvement over the current 2017 version. There are a lot of changes, and total units are down from 6058 to 5346. Performance is much improved. Lots of corrections...it is going to require a fresh download when completed. One thing that's being adjusted is tech trees, especially for European NATO. Era 2 Mobilization will focus on your heavy land units. Era 3 gives you access to oil, military alliances with neutrals, and surplus equipment from the U.S. Era 4 will not just give naval, but also some air and light ground units. While working on it, I was reminded of the Wargame series where you had "decks of cards", and the available units were based on your deck. In the scenario, this is essentially the choice between giving preference to the Army, the cabinet, or the Navy/Air Force so to speak. So, the U.K. for example has light infantry, aircraft, and deployable units along with naval units in Era 4. Basically the idea is to make it more rewarding to choose your tech order, so that maybe you want to grab a few from each era, or plow through one particular era for the end bonuses. Right now I think it's too easy to just get oil and then race to Total Mobilization. Warsaw Pact of course is locked in one era, but this is to represent their more comprehensive and less schizophrenic mobilization plans. They are getting some nice bonuses and a more streamlined unit structure. Lionic had some great input here so expect more interesting choices and the addition of some Delta and Gwendoline units.