Ground forces should have SOME ability to knock out planes. Fighters/dive bombers doing low-level attacks had to face machine-gun and even rifle fire which was no fun in large quantities.
We can’t forget that ground forces normally had some heavy AA (in British forces these were often a Brigade of 3.7s attached at Corps level). So there should be some small chance of taking out aircraft with ground forces; maybe 11+ on D12, or 1 D6 for every 2 ground units?
I reckon this is where the AA guns come in; they aren’t all that effective but they are pretty cheap, so you should be able to buy some mobile AA and use them to protect your ground forces from aircraft. A good NA is to allow Germans to use their mobile AA (which would include many 88s) as anti-tank. Then again I reckon we need anti-tank artillery units anyway (cheap, good in defence against tanks, bad against infantry) as this will reduce the power of tanks.
Out of interest, considering the duration of a turn (3 months) the fact that planes have to reload is not all that serious, is it, since so does everyone else over that sort of period. However, only allowing them a few rounds is quite a good idea because it sort of allows for the fact that it takes an enormous amount of supply to keep planes flying.