With all the talk of a new strat system, I finally decided to try and organize my thoughts and write up something I've been milling around for a while.
First the problems, these are pretty well known so I won't go into much detail. Strategic targets now play a minimal role in the game. The strat city is the best defended target on the map. An attack on the target almost guarantees 1.5-2 hours of flying and a couple 163s, and for what? Any significant damage to the strat usually means that country will take notice and send multiple goons in to drop supplies back on the city. By the time you land, the strat is usually back at full and your effort means nothing.
Here is a quick illustration of what I'm thinking. The green and blue dots represent strat cities. I love the strat cities and want to keep them around but I want to mix it with a bit of a zone system. To clarify, the zone system could just be the same city design we have now. Ignore the actual city icon on the map.

Maps would be split into zones (indicated by the green lines), three or four seems to fit well for a large map. Countries would still retain a strat complex at the rear near 163 bases.
This would build a supply chain, from the main strat complex, to the zoned strats, to the fields. I think programming in a more significant impact would be in order for damage to the strats, not drastic, but enough so that we don't run into the same problem as we have currently. Bombers would have incentive to travel to the zone strats, but not necessarily at 30k+; and fighters would have incentive to protect strategic targets along with knowing they won't need to climb to 35k+. An attack to the zone strat reduces ability to resuppy bases. And an attack on the main strat complex will reduce it's ability to resupply the zones, and in turn the bases. So the main strat complex is still a lucrative target but that comes with a much higher threat.
Similar to the current "retreating strat," a zone strat would eventually retreat or more appropriately "abondon" the city. Supplying that zone would then become the main strat's responsibility. I think this would help prevent steamrolling because now the strat for those bases in that zone is the well defended city in the rear. I'm not sure the best way to address advancing fronts. Would their zone city just be responsible for the new captured bases or could an advancing army capture a strat?
I think this could also present an excellent opportunity to put in more and better rail systems and/or convoys. Levels with water could incorporate oceanic convoys. Large scale convoys could travel in between the strat cities to represent the re-supply. For example in the above picture, let's say bombers attack the eastern strat city. Re-supply convoys would come from the central strat and the main strat complex. This gives more strategic targets, while making a complete choke-hold of supplies very difficult (although not impossible).
Don't look too much into how I drew up my map, it's just to demonstrate concept.