The strategic and supply system changes in the latest AH patch (1.08) have lessened the impact heavy bombers have on game-play to the point where I wonder whether flying one is worth the time and effort.
For example, Bishops and Rooks were fighting over a base. I decided to bomb the base that most of the Rooks were flying from. I took a Lancaster to 24,000 feet, got over the target base, and on my first run dropped on two fighter hangars. I got two "destroyed" messages, turned around and dropped on the last fighter hangar. I got another "destroyed" message and decided to hit the barracks on my last run.
As I was looking through the scope to line up on the barracks, I noticed that all the fighter hangars were up already! This was less than 5 minutes after I dropped on the last hangar. I looked at strat and sure enough, fighters were enabled for that base. Obviously someone had gotten an M3 from another base with a nearby spawn point and dropped supplies.
During the time I was in the air, en route and over the target, the Rooks had managed to get 3 of our bases in sneak captures - where it appeared that maybe only one or two rooks were working the bases that were captured. It was very discouraging to say the least. I could have been more productive flying C47s to the city, hoping to sneak one in eventually.
I like the idea of the new supply system - the trains, depots and stations - but what happens in the game is if you see a base that isn't 100%, you just fly or drive supplies in, so the system is irrelevant to that extent. It doesn't matter if the stations are 75% destroyed, or who owns the depot, or if trains arrive because one C47 or M3 can take care of any damage.
What I would suggest is that supplies NOT cause buildings to instantly re-spawn. I think it makes sense that supplies instantly bring back to 100% things like ammo and fuel, but buildings have to be re-constructed and that takes time. The same thing should apply to HQ - I don't think supplies should instantly rebuild it. This would bring back some of the impact bombing had on game strategy.