Small thing, would make gameplay more realistic: bombers don't actually get to fly around the map willy nilly, but are based in cities. So on your turn you can select a target within range for attack, and if the city is attacked catching the bombers on the ground combat proceeds as normal and the bombing run does not occur. And next turn, if the attack occurred, the surviving bombers are back in the city.
This nerfs certain aspects of the bomber and boosts it in others.
Interestingly, the idea could be extended to naval units by setting limits on how long they can range about: it's more complicated to work out realistic rules for a navy, though, so I'll leave off of that for now.