It is so rare these days that ENY shows up that I don't really think a "multiplier" effect would do much good on ENY. That is better on regular strats.
I want to see strats be worth something, and I think the idea of strategic "factories" is a good one. Right now, all we bomber boys do is just flatten bases - it gets old fast.
Frankly, the strategic factories we have now (AAA, Radar, Troops, Fuel, Ammo) could be made immediate targets just by having a direct and immediate effect on the respawn times of strats at bases. For example, if you are blasting radars, they stay down 45 minutes with 100% of the radar factory up, and add the percentage of the destroyed strat/100 as the modifier. So with 10% of the radar factory destroyed we have 45 minutes x 1.1 = 49.5 minutes radar respawn time at bases (either countrywide, or by zone if we get zone strats back), and all the way up to 90 minutes with a 100% destroyed strat. This would work on barracks (troops strat), AAA (aaa strat), fuel (fuel strat), and ammo (ammo strat) independently. We can allow direct resupply to continue at individual bases as normal this way, but it gives some real meaning to strats in the tactical arena.
For the City strat I would suggest just adding +1 to ENY for a country for each 10% of the city destroyed. If we get zone strats back, this could be applied to every base in that zone only. This makes it worthwhile to run a big bomber raid on the City, because if you can get it 60% destroyed you can keep the 5 ENY planes down until it rebuilds. With the City 100% destroyed, ENY gets to 10 for that country (or zone) until it rebuilds.
The HQ is still problematic - I hate the idea that it can be resupplied at all. I would suggest setting it up so that wacking HQ just destroys the DAR BARS and not the dot dar at bases with an operating tactical radar. You lose the strategic picture, but still get tactical alerts from operating radars in the field. We could try this along with prohibiting resupply of HQ and see how that works.
What I really want for Christmas is for HTC to at least experiment with some of the settings and work on making strats worthwhile. Another setting that might be nice to get changed is the ord requirements for ammo bunkers (raise to 500 or 1000lbs since this is supposed to be a hardened bunker).
$.02