yoshi, while no one has figured out how AA works in the first place (other than more is better), it seems that it is not overpowering game-wise. Having a SAM in a city does not prohibit using bombers against it.
Historically, the ideal is always to have air supremecy (air superiority) to cover your important ground units. Flak/SAM are there for backup for when your fighters are not available.
The trick, of course, is to get into a tumble with someone where you have an interesting air war going on -- those are rare gems!