Leave the score system in place. Tweaking it to factor in ENY as previously discussed in this thread for the sake of evening the scoring field is a good idea. If you don't like score/rank, ignore it. If some idiot dweeb thinks he's better than you because of his score, go all DA on his derriere or better yet, don't care what he thinks. If you think the scoring system is responsible for dweebish flying I disagree. People kill you because that is what they're there for and they will kill you any way they can because defeating futile attempts at survival is what we find amusing.

Leave the perks alone, it basically serves its purpose. Go a week seeing a 262 for every Pony and you'll be happy for a couple days because you'll have a free 262 as well. Then what do you think will happen? You will start missing your sentimental newly uber uncompetitive plane X and get frustrated. Variety is the spice of life.
When I drop a bomb on something I want it to go boom. No spontaneous structural regeneration crap if I die.
If we want to see strategy we should have incentive to fight a war. The basic incentive to fight a war is the ability to win it. Map changes every several hours do not permit this. Is there a point to capturing bases right now that someone isn't telling me about? A vulch is fun but does nothing except pad stats.
Change towns so they do not regenerate (but allow AAA to regen post-capture), let a team leave a satisfying wake of destruction in the scarce few hours of fighting on a given map. Front lines will take battle damage, change faster and no bomb runs will be wasted. "Porking" a town will have meaning for bombers instead of simply being a dweebish waste of time 90% of the time.
When it is time for the map to change, the game should flash some stats from the campaign and declare a winner for the engagement (taking relative player levels into account) instead of just kicking everyone.
The game should track map wins by for each country over the course of an entire tour to give country loyalty some vague form of meaning. To give players a little vested interest in helping the greater cause, give them some general use perks for base captures to use as they see fit. (IE I don't fly buffs but find the B-29 is appealing) Said perks could be used in any category and transferable to players who care about perks. For those who really care about winning the war but understandably see goon resupply runs as boring, let them spend these general use perks strategically to regenerate the damaged towns that would not regen otherwise.
As far as stopping the "bomb and bail" crowd, I don't think this is a huge issue, it happens a minority of the time. Also, while I've never done it I can understand the temptation. Buff sorties get shot down a majority of the time, take mucho time and there is little incentive to wasting your day driving your virtual buff a half hour home after you've gotten your perks. Most of the time these folks just provide easy kills for the rest of us. That said, there are more "realistic" options to control this dweeb behavior. IE: If they bail from a perfectly good aircraft, throw a modest perk fine at them instead of rewarding the sortie with additional perks. If someone still does this despite the perk penalty I say let them- if they aren't doing it for themselves they are doing it for their country's war effort with the limited time they have online.