I don't think balance must be the focus here. Balance in singleplayer games is not a priority. I'd even go as far as saying certain imbalance provides even more fun.

And if we do want to take multiplayer into consideration there is always the option to houserule out certain imbalances.

The Dominions 5 comparison flies well again here. 

This entire discussion embodies a question I asked in the first Q and A, although I didn't word it in the way I meant - the way I asked the question was basically "How do the devs decide where to devote their time and resources?" when actually what I was getting at was "How do the devs decide to prioritise things that aren't - if you're going to be strict about it - actually 4X ideas, but are more RPG/RTS/FPS mechanics/ideas?"

It's probably simplest to create a Galactic Civilizations that is a very, very, long and very, very complicated bunch of questions that it asks the Player:

Ask Question 1: Pick 1 of 3 options.

Ask Question 2, based on the option picked on Question 1: Pick 1 of 3 options.

Ask Question 3, based on the options picked in Questions 1 and 2: Pick 1 of 3 options.

And on and on ad infenitum....

But it wouldn't make the cash registers ring, now, would it? Hence, graphics and sound and cutscenes and designers etc...

After spending tons of time in both GC2 and GC3, and now starting in GC4, I'd have a couple of thoughts on the combat system:

1. Yes, ship roles. But, as pointed out by @tid242, they need to be descriptive, not one-worders. And it would be VERY nice to be able to set them at combat time, NOT be forced to pick one for a ship for all time.

2. Consider varying ranges on weapons by weapon SIZE, not TYPE.   That is, weapons that require a lot more size can reach much further. This only makes sense:  a PDC doesn't have the range of a railgun, and a larger missile should mean both more room for damage AND more for range (fuel).

That means, you essentially end up with weapons classed for small ship, and those classed for large ships. You're not going to find a Wave Motion Gun on a fighter or even corvette. Ion cannons belong on mid-sized frigates (taking up most of the space) or destroyers (with a small array of them).  Laser cannons are for Fighters, as while they might do decent damage, they absolutely shouldn't have even a fraction of the range of either the WMG or Ion Cannons. 

So, every weapon should come with four stats:  (1) size (2) damage (3) range (4) rate of fire/recharge time.

It should be entirely possible to have both a Large Kinetic Railgun and a Wave Motion Gun with the same range, though their size/damage/rof might be different. Just like it might be possible to have a Small Railgun and a Disruptor Bank with the same range but much shorter than the WMG.

Small ship should simply NEVER be capable of mounting large weapons, and small weapons do poor damage relative to their space requirements.  E.g. a typical small weapon might do 3 damage and have a 1000 range for 7 spaces, while a large weapon might do 15 damage with a 2000 range but require 30 spaces. Where a small ship can't ever exceed 20 spaces, and a large can have 100. 

Basically, there needs to be a distinction between CAPITAL SHIP weapons (with much larger damage and range and huge space needs) and FIGHTER weapons (small damage, small range, small(er) space).  In general, I vote that the former have much longer range and damage and higher damage/space ratio, but have a significantly poorer ROF than the latter. 

3. Defense types also need variety. Particularly the recognition that individual defense methods can be useful (to different degrees) against more than one attack type. 

My take on this is that a particular defense technology can have Strong against a type (1 x Rating) or Weak against a type (sqrt Rating).

So:

Shields protect STRONG against beam, and WEAK against Kinetic, and not at all against Missile

Armor protects STRONG against Kinetic and WEAK against Missiles, and not at all against Beam

Ablative Armor protects STRONG against Kinetic, and WEAK against Missiles and Beam

Chaff protects STRONG against missiles and WEAK against Beam, but not at all against Kinetic.

PDC protects STRONG against Missiles, and not at all against Beam or Kinetic, BUT it might have a low (short range, low damage) OFFENSIVE capability.

And so forth.

Also, I want to get away from the GC3 idea that defenses are used up linearly - that is, if you have a defense of 5 and take 2 damage in a salvo, you only have 3 left. I don't want to go to the GC2 method where defenses regenerate completely every time. Rather, I'd like to use a middle ground:  at set time periods during combat, a defense gets 1 point back (that's 1 PER defense thing, so if you have 2 armor placements, each gets 1 back at the set time). That is, all defenses regenerate not-too-slowly over time.  This gives a LOT of incentive to put defenses on ships, whereas in both GC2 and GC3, the primary "Best Strategy" was to solely load up on weapons and ignore defenses. This means it gets hard

And yes, larger ships need the ability to target multiple different ships per salvo. I like the idea of a "battle computer" that increases the number of ships which can be targeted per X seconds. 

More or less, the expectation is this (per ship size):

TINY ships mount 1 or 2 small weapon systems and very small defenses

SMALL ships mount 3 to 4 small weapons systems and/or a small defense, potentially against more than 1 attack type.

MEDIUM ships should mount 1 capital weapon and 2-3 small weapons and a medium defense against most attack

LARGE ships should mount 3-5 capital weapons and 4-6 small weapons and a medium defense against all attacks or strong defense against one.

HUGE ships should mount 5-10 capital weapons, 5ish small ones, and a strong defense against all attack types.

The penalty should be that the larger the ship type, the slower (tactically) you can possibly go. Bees vs whales and all. 

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The jist is that we want out of the straightforward Rock-Paper-Scissors stuff, so that combat is MUCH less obvious as to the winner, making it more of a gamble (and thus, the Ship Roles being more important).