I like the idea of bombing resources to reduce their income (or just reverting them to neutral to simulate the loss of infrastructure/facilities?) but I'm not sure the game, as it stands, really needs any engineering type units to upgrade resources, as we already have city-based facilities that already accomplish this.
But then, given the speed, range, and relatively short build times of even mid-tech aircraft, this might make aircraft in general a little too powerful and versatile.
Like someone above said, perhaps the answer can be found in not "city-spamming" quite so much. Grab the key ones and all the resources you can safely hold, and leave a few for later, when your economy is strong enough to subsidize those other towns.
I'm playing a larger game right now, and I've run into a few walls where I've realized my economy wont be able support my rate of territorial and military expansion. If I were to continue building in every city and researching at the rate I was, as well as capturing new cities, I would have been left crippled.
So I compromised. I decided that I didn't need a garrison in every city, and that I didn't have to blitz through every tech in the tree. I disbanded more than half my ground forces. I stopped using massed assaults and started focusing instead on doing the most damage at the least cost. I focused more heavily on scouting and using paratroopers to capture weakly protected towns and resources.
And so far it's working perfectly. My economy is stable, my research is back on track, and I'm able to integrate newly taken towns without having to rely on trades.
Brute force can work, but you have to have the economy to back it up. If you don't, fight cheaper, and don't conquer every town you see just because you can.