I'd just like to see each ship have a more defined role, really.
Right now battlecruisers/battleships are good against everything, and really have few weaknesses. Even bombers have a tough time taking them out due to the sheer firepower a battleship commands.
On the flip side, gunboats are effective against nothing (with a few exceptions *cough*BH gunship*cough*). They're not great against fighters as they lack the agility to keep up with them. They're not great against capships as they lack the firepower to do any real damage to them. They're not great against bombers - who both out-manuever most gunboats as well as have more firepower.