I have an idea I worked a bit on to this end. I'll post it in the next few days, but the key is to tie strats to how easy it is to capture bases and have the duration of the effect of a raid be long enough to make it worth it. Basically, if strats aren't damaged the town buildings and guns should either be extremely durable or repop extremely fast, making it very hard to do a capture. The further down the various strats are pounded, the easier it gets to keep the town down enough for a capture, in addition the strats would retain their current effects.
This would also be a strike against milkrunning in EW and perhaps make bombing town centers less effective for points and perks.
I know I should wait until you post your complete idea, but...
When you make it that difficult that even capturing bases without any defenders would be hard to accomplish, the gameplay effect will also be huge in the LW. May be too huge. Because in that case, bombing strats is almost a prerequisite to capturing bases.
I see two problems with this:
First, the rate of captures will slow down considerably again, which in turn has a big impact on the "war" and map rotation in particular. You would have to change a lot of other gameplay settings to balance that again.
Second, what about a country that has a lot of territory on a large map? Do they ever have a chance to strike back, when enemy strats are basically completely out of their reach?
Not shooting your idea down, just a few things that came to my mind. I'm eagerly anticipating your fleshed out idea
