We've considered this. Honestly, the rapier isnt 'useless', just out of vogue. If you compare its hp/cost and its dps/cost it is incredibly good (and very fast, compared to land), and is still a prime candidate for massing in FFA. Its stats required to be an AA unit just make it very strong against land. We may still go this direction if we cant find a place we are happy with, but the HP nerf seems to have put it into around about the right range.
Banisher can and does hit planes. It will shoot down bombers (though it -is- possible to outrun). People just dont use banisher very much because its riot capacity isnt all it could be, but it will absolutely gib gunship swarms.
If i designed zero-k from scratch, i would adopt the XTA model (minus the special damages) where everything hits air and land- IE, no dedicated AA. Defender was meant to be a 'test-trial' for this change, but the balance (esp air balance) got too static and stable to continue down that path. Even recently, the air change that reduced the HP of planes and the damage of AA is also an attempt to go this direction (moreso to make air-hitting ground weapons like slasher better vs planes- didnt work for slasher though).
However, this redesign would require a fair few changes. Firstly, AA needs massive range because air is so god damn fast. In BA, air is way slower, and AA is consequently much shorter ranged. When you consider that the Krow moves faster than a BANDIT (and its one of the SLOWEST air units!) there is a lot of room for this. This makes AA that can hit land act like artillery, and because it is perfectly accurate, it cannot be given the usual weakness of artillery, IE inability to hit mobiles. So firstly, the standard static-defense would have to be fairly long ranged to not be outranged by AA (more like the current defender than current llt- again, XTA style). If planes are made slow enough (even slower than land units- look at Starcraft say, where planes are not much faster, and the endgame tech planes like battlecruisers are actually much SLOWER than land units) this range bonus isnt really needed as much. However, that would impact on the current scheme of refueling planes- it would drastically increase their reload time, thus increasing the damage they'd have to do on one run (or having to increase their survival or some other attribute).
So yeah, this would require too many changes to the balance to do at this stage.