If the factories are much further back and much easier to supply, then there accrues no great advantage to hitting them. There would then be little incentive to hit factories at all. Better to use the bombs at the front line. The score guys would still be heading there at the start of each month (probably in another arena anyway), but I can't see an increase in activity high over the factories from this, just a decrease.
How about having the strat sites (assuming there's multiples for each type) have some sort of scaling effect? Have their contribution to the country resupply be e.g. 15% at front lines, 25% midway, and 60% for the rear-most strats. Would such a scale be enough?
If not, how about having the rear strats be parent strats, in that they resupply both the dependent (rear) fields but also the strats midway and at the front lines?
Another component could be supply lines. These could be more meaningful if they were the only means of rebuilding strats. The supply routes themselves are too easy to disable in a setting like the MA (a few intruders NOE can sabotage things undetected in the countryside real quick), so they could stay immune as now, as well as their spawning hangar; unless it had adequate defense like a VH and radar tower (all the country's supply hangars and accompanying objects' down-time would depend on the rear-most City). If only the supply convoys themselves are vulnerable, then they could be made either more numerous: e.g. the same number at fronts, ~twice as many midway, and twice as many and/or twice as often at rear fields. The only feasible exception that I can imagine off-hand would be bridges with at least some kind of radar (maybe not dot-dar but just flashing) and a minimum of automated defense, or some GV spawn. Obviously, bridges or other critical points like these would have to be few and well placed. Maybe make the rebuild time for these depend on the main City as well.
Altogether this could make a front line strat neutralizeable by destroying it as usual, and destroying the convoys (from their own supply line + the parent strat's supply convoys) which would run at a relatively low frequency (the parent supply convoys could be easily differentiable, e.g. heavily armored). While at the other end of the scale, hitting the major strat site for any strat type (way out near HQ), as well as the major city (if there are multiples) would effectively kill the whole country's strat of that type, while then depending on the resupply convoys (with indestructible routes and hangar) to bring it back up. And these would be fairly numerous so that you could only suppress rebuilding of the city, and in turn rebuilding of the parent strat type, by having a large or undisputed presence deep in enemy territory. The payoff would be a relatively but arbitrarily large aggregate downtime.
This could be all scaled by the relative "weight" of each strat (like the above example, three strat levels 15, 25, 60%), and by the number of strat items of each type on the fields themselves.
One of the possible positive effects of this scattering of critical points (while keeping one large target as center point) would be to split up attack forces in the arenas. You would have to have bombers or very large fighter-bomber groups for the strat sites, and have to send smaller units to intercept the convoys. The parent strat convoys would probably best be quite a bit longer than the trains and truck lines we have now.
One flaw is that the above system effectively removes player resupply... Only for strats though. Fields still are affected by player resupply. I suppose the HQ and rear-most City would also best be left available to player-resupply.
