I think a big problem is that one side is usually getting ganged up on. There needs to be something to balance that out. Either give the side getting jumped SEVERLY reduced perk prices (as in 50 perk KT's ) or wail the crap out of the two attaking sides with the ENY-stick. Spit V's, P-40's, and 109G2's.
But I wouldn't mind base taking being strategic rather than the end goal of the game. Only problem is how do you detirmine when the war ends? It would be kind of nice if we could have a major strategic goal (say capture the enemy's capital city) and that wins the war for you. But the issue is that we don't suffer from starting populations and attrition rates that would limit the action we could take. We also have no worries about logistics or any of the issues that woule keep us from launching a counter-offensive on the flanks.
Ganging is probably a problem that cannot be fixed with three countries in play. I've seen countries get ganged even with fairly even numbers, so I don't think ENY would fix that either, it's just a matter of which country each side decided to attack.
The long and short of this comes down to human nature. You're not going to get rid of large mobs of planes flying together, because that's why people play this game in the MA. Those that want small (1v1, 2v2, 3v3, etc.) fights fly in the DA. The spontaneous teamwork is very appealing; it really doesn't take a lot of effort to band together in this game.
You can't forcibly deter hordes either, because then people will feel like their ability to play the game is limited (which is true). Something that naturally causes both sides to group up and fight each other is probably the best solution. But then the three countries thing comes into play, and ganging is once again possible.
I don't really see an obvious solution.
However, if we dropped down to two countries, a lot could be done, in my opinion. You'd immediately rid of ganging (ENY would control unbalance, for the most part), and you could create a series of capture points inside each country's boundaries that must be taken in order to win the war. This would give a common attack and defense point, while still creating a reason to tread into enemy territory.
However, I seem to recall that HTC stated they would never get rid of the three country set-up, so that might be a dream.