Sounds like it is time to sit down and reappraise the role of all ships. If they aren't useful, there isn't a reason to have them in the game, after all.
That, or consider going to a custom build model, with the cost of ships to make based on the cost of parts + mass + inefficency.
I know they want to stay away from that, but this pass of Battle Hammers and other ships being so changed does show that their is loss of understanding why ships are in the game in the first place.
Say, base cost of a ship is X, that gets you ATT 0, DEF 0, Hit Point 0, RANGE 0, Sensor 0.
For every +10 Hit points, cost 50 production.
For every +1 Attack, costs current HP in production.
For every +1 Defense, costs current HP in production.
For every +1 Sensors, costs 10 production.
For every +1 Range, costs current HP in production.
What can I say, I like costs linked to BASE hit points. It's a good representation of size of ship, after all.
You'd need to retool the techs a touch. Phasers get you the ability to ADD attack to your designs in the first place. And top out at say, +5 or so. Other techs could get raise the top, or reduce the cost for that category. So, Battle Shields, for instance, would bring a reduction of 50% to the costs of Defense, and let you top it out at +10 from before. etc etc etc.
Just a suggestion, but then your balance points are easy to find. If you need a raider ship to go chase down and kill freighters and transports and constructors, you can design the old corvette equivalent. Something with just 10 HP, Attack 3, Def 2, Speed 3, Range 3, Sensor 1 at the cost of er... 120. Humm... Well, I suppose tech benies for being up on Attack (if it stayed in place) would reduce that to 105 to 110 or so... What's the original cost of Corvettes?
The AI just has to learn to build ships by roles needed.
You could let the computer have the fun of giving you discounts, slowly, on ships designs you continue to roll off. Scale of volume returns/logistics.
Just a long, oddball thought of mine. I'm not looking to 'Moo-ify' GalCiv. Just address all this shifting about wildly of ships and their balance.
After all, Star Fighters SHOULD be worthless, according to the techs. It's mean to let you shoot up constructors, frieghters, and other star fighters, right? Defenders are meant to be the first defense ship. There to keep out enemy transports, right?
So we either need to focus in on customizing ships so that they will always balance themselves, based on costs to build out of parts, or we can focus in on the roles of the ships, and suggest they be adjusted to fit those roles. Yeah?