I'd like to see the HQ go back to the staged destruction method where it could be only patially down. I mean what's the point of all those buildings at HQ? All you need is the one hard building now. I also don't think it should be able to be re-supplied.
As to fuel I'd also like to see the old progressive fuel destruction come back. 25% and can't fly far? Up further back or take another plane with higher capacity. I'm pretty sure that during WWII when a field's fuel tanks got porked there were repercussions. You could still allow drop tanks (filled at 25%) as a partial off-set. As an alternate you could limit the number of planes that could lift from that field.
As to barracks, field acks, etc. there are just too many now. I never used to use field ack for cover but now I know that if I can drag some sucker in and make him turn just once it's a quick, effortless proxie. Forget the field ack, the town ack is plenty for a quick proxie. And why all the barracks? Next we'll see 5 radars per field because, my god, they keep taking down local radar.
Finally, the old strat system on the large maps was great. You'd almost always see the strats go before the field captures began. Now it's a joke and very much because of the changes in the field lay-outs (too many barracks, acks, etc.). I will say however, that it makes for easy milkrunning in the LWA's as there's a general feeling that there's no need to defend the strats (fuel strat a case in point... what does it affect?).
Oops, sorry, one more thing. Bring back the old calibration method for bombing.