1. Reducing all capital ship shields so a group of two or more fighters/bombers can disable it much easier. Longer recharge time and fewer batteries. This will mean fighter protection will be essential if you in your capital ship encounter enemies flying fighters and bombers.
2. Increase torpedo (excluding the already overpowered ones...) and class 9 missile explosive energy and radius.
3. Increase capital ship hull and firepower on destroyers/cruisers and above. Reduce rate of fire and/or velocity on turrets, cruisers and above. Other way around for gunboats, increase rate of fire and/or velocity on turrets, decrease hull some. Perhaps lower normal flight/cruise speed for cruisers and above. Armor upgrades for capital ships could be lowered or removed completely.
4. At least double the price (or as suggested, a capital ship license) of destroyers/cruisers up to the already quite expensive battleships. People will trade more, more potential income for the poor pirates.
People will be probably be spamming gunboats, but a gunboat won't stand a chance against a group of fighters without support. The thing I've noticed is that unless you're up against anti-shield equipped bombers or capital ships, you'll feel perfectly safe alone in your gunboat. With better fighter torpedoes and lower shield power/hull on your precious gunboat, you'll not feel safe ever again.
My characters on Disco: [LN]-Andy.Doggett, The.Flying.Betty, Russ.Dalton, Harald.Treutiger