I know it's not being looked at it from this perspective, but I really think in order to make these things work in a reasonable and logical manner we need to take a step back and look at combat in general.
If the idea that a 'normal' type ship is going to have one of three traits - heavier on energy weapons, balanced weapons mix, or heavy on missiles, then we should assume that a ship should have 'average' defenses against both long-range missile attacks and shorter-ranged energy attacks. Roughly speaking, a ship of the same tonnage is it's equal, thus it should be able to go toe-to-toe with it's equal for at least a few rounds. An unbalanced mix of energy or missiles means that it's defenses can be breached faster, thus forcing the ship to break off earlier or it will be knocked out of action earlier.
A squadron should act and fight as a single unit, so if we use the defensive rule as stated, a ship can fully engage with it's defenses for missile aimed at it, but can only draw upon half of the missile defense from every other unit in the squadron. By default a squadron of ships would deploy themselves to maximize their defense postures, so that should always be assumed as part of the equation. If we are going to have a trait of Fleet Defense, we need to make some other assumptions as well. Those being that fleets allocate their offensive fire in a group effort, and their defenses as a group effort. Because we are talking about fleet combat, we really don't care about individual ship stats, just the squadrons. So, like fighter groups, we should assume that the squadron is going to roll up its offensive/defensive firepower into attack and defense rolls. An easy rule o f thumb would be that it gets one attack per ship, and it can target one ship with it's attack. Damage to the squadron is allocated say 50% to the intended target, and the rest spread among the squadron. You can still burn down a single ship, but you might find it harder to do so. And to make it less likely for rules lawyers to make damage sponges, all ships are treated equal to the lowest armor factor in your squadron when allocating damage among the rest of the squadron. So if your missile cruiser with very light armor to pack in the missile launchers takes 50% of the hit, your heavy armored beam cruisers don't get to take advantage of their much tougher armor (one could say by taking damage meant for another ship they give up certain defensive traits).
Your defense against missile attacks would be based upon the overall fleet defense rolls, which seems better than trying to keep track of indvidual rolls and ships. The bigger question comes to rolling up the damage, how to do you take into account various weapons and traits without bogging things down a lot? It seems we are either stuck with a complex individual ship combat (and keeping track of missile salvos travelling at distance) or a very abstracted one, which blends the off/def capabilities of a fleet into a single entity. They both have their pluses and minuses. Question is, where do players see this going?
