I do like the economic site of balancing. With drydock/shipyard and a cargo system, fielding a titan in the first place would be a sign that you talk serious business, and loosing it would be a major setback for any faction. Contrary to that, fighters would be throw away things you hurl at your enemy in spades because rebuilding them is easy and inexpensive.
And this is were the actual balancing between ships should be in my opinion: A big ship with adequate point defense weapons should be a tough nut to crack for fighters and bombers, but remember the key thing: Every point defense weapon you put on your ship decreases the amount of anti-capital weapons you have on it, just because there is only so much space on the hull. So a cruiser decked out with anti-capital weaponry (unguided missiles/big cannons for example) would most likely best another cruiser that had more mixed weaponry and would definetly destroy one that is designed with pure point defense in mind. Of course, that cruiser would probably fall victim to fighters itself. Specialisation at work.
For this to work, dedicated point defense weapons need to be straight up better at destroying smaller targets while non-point-defense weapons need to be great against bigger targets without the two musling on eachothers turfs. One thing that springs to mind is the system from Masters of Orion 2 (great game, btw). You could directly assign weapons as point defense or heavy mount (was it called that?).
How that could work in Starmade (I am writing with turrets in mind, as we are talking AI against AI):
Every turret (not the weapons themselves) has to be assigned to be either heavy mount or point defense. The effect applies to all weapons in that turret.
Point defense increases projectile velocity (less effective evasive manouvers, pew pew), reload speed (you need to take down many targets fast), turret turn speed (keep tracking, those fighters are agile), missile lock on speed (less tracking, more shooting) and number of shots in shotgun weapons (more fire in the sky... space). This all comes at greatly reduced damage values per shot, still enough force to be dangerous against targets that are smaller than your ship (assumption being that turrets and their weaponry scales upwards with ship size), but low enough that its only a minor annoyance to anything around your own ship size or bigger.
Heavy mount, on the other hand, decreases reload speed (less pew, more boom), projectile velocity (you dont need speed, the target can barely turn), turret turn rate (see velocity) and lock on times (see velocity also) while boosting damage greatly. All of this should make sure that these turrets arent effective against larger numbers of smaller vessels, while giving smaller ships weapons that can actually hurt their bigger cousins.
Of coarse, a small ship will still be utterly wrecked if it gets hit by a heavy mount (lock on) missile, but the combination of low turn rate, reload speed and projectile velocity/lock on time should make sure that point defense would be more suitable in that situation. Something else i thought about was to have the range be a factor, shorter range for PD, longer range for HM. But then again, i dont even know if weapon range is currently a thing, it doesnt look like it is...
The last thing I am unsure about is what to do with a ships main weapons. Make them the same thing? A fighter with heavy mount (slower, more ponderous but with more boom in slower intervals) against a fighter of the same type with point defense (nimbler, faster firing, less boom)? Or just the jack-of-all-traits middleground weapons the current weaponry would turn into? Or the ability to assign the weapons on the main ship on their own?... I dont know, suggestions?