I think it is important to ask: "How is a well-balanced weapons system going to lead to more interesting gameplay decisions?" In my opinion, the answer is "not much".
There are three possible results from a missile rework:
-Missiles remain inferior to the other weapons. Everybody keeps using the other two weapons systems.
-Missiles become superior to the other weapon systems. Everybody uses missiles.
-Missiles become equal to the other weapons systems. It no longer matters which weapons system you pick, the choice becomes purely based on whether you like "whoosh-boom" more then "dakka dakka" or "zapzap".
None of these outcomes lead to meaningful choices and interesting gameplay. Perfectly balanced weapons are not interesting weapons. I think there are other possibilities that will lead to more engaging gameplay regarding weapons:
-Each weapons system has its own defined role, which is based on play style. For example, missiles could be made cheaper, while PD is made more expensive. This would make missiles a good early game rush weapon that falls off at a later stage. Energy weapons, on the other hand could be expensive but powerful, which makes them a poor choice for the early game but a strong option for the late game, for those empires that want to turtle a first and then later steamroll all the missile plebs with their superior weapons.
-The information on which empire uses which weapons and defenses, and an AI that acts on this information, for example by being more likely to attack an empire that has weapons it can easily counter. This way, the relative power between empires is not just determined by fleet strength and tech level, but also by how well their tech counters yours. This leads to interesting gameplay because you will have to take this into account when you select allies and enemies. How cool would it be if an empire asks you for an alliance, not because they like you but because "our archenemy uses missiles, and you have point defense, and we don't." This could be combined with a more restricted tech system, where it is harder to have a counter to everything and picking your battles wisely becomes more important.
I think that strategic combat is never going to be a strong point of this game. The strong point of Stellaris is the ability to create your own species, and play out their story among other species in the universe. Having a balanced weapons system is not going to improve that experience. Tuning the weapons to match different play styles, or having different weapon technologies have various implications on diplomacy and relations between empires, will improve upon the strong points of Stellaris, and will help to make it a unique game in its genre.
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