In a tweak to the original idea, how about make it even more "Capture the flag" like, and... well... kinda like this...
HQ contains a flag, and is surrounded by the cities that are currently used as Strats, including the flak towers, etc. To "win the war", you would have to land at the enemy's HQ with a C47, drop 10 troops, they'd run to tower and all 10 troops must survive, 60 seconds later, run back to the C47, and you'd have to successfully land with the enemy flag at one of your own airfields.
Maps will always state what sector the flag is in, but not where inside each sector. When your team's map is taken, the 163 is enabled at the closest surrounding friendly airfields to the HQ.
What this does is put a risk vs. reward system in for everyone. Do you try to sneak the flag from many airfields away? Do you capture all airbases on the way to the enemy HQ to make the egress a much shorter distance? It gives a lot of work for the bomber guys to do (take out flak towers, all hangars), attack guys and GVs (if you captured the bases close to HQ - take out local ACK), and puts risk of sitting your C-47 on an enemy runway for some time. (obviously you'd want to take out all hangars for this maneuver). It would allow the defenders ok defense with the heavy AA outside the HQ, as well as the fact that all you have to do to "reset the flag" is to shoot down a slow goon. Also makes the bases immediately around HQ that much more important. Also puts more emphasis on a moving battle line, to try to stop deeper penetration instead of capturing bases like ports irregardless of what's going on around them.
This is not a criticism on current gameplay, just an attempt to tweak the OP's idea a little. =)