To achieve having both huge epic style battles and ships with strong personality at the same time there could be few hero ships and huge amounts of faceless non hero ships. The hero ships would have strong table turning abilities and also strong defenses so they don't get nuked right away too easily. The heroes would gain experience enhancing their abilities and personality while the rank and file type ships does not. Perhaps they would also be more extensively modeled with destroyable components, energy managment and such. Maybe simply integrated with the special abilities, like an ability to increase firepower for a short time while engines are cut to model "power to weapons".
I'm liking where this is going. At the risk of overloading the programmers, it would be nice to have commanding officers (CO's) created when the ships are created. If they do well in a battle, they gain experience, making their ship more efficient. They are able to recieve promotions to larger ships, taking their experience with them. During battle, there is a chance that the bridge is hit and the CO killed, and of course if the ship is destroyed.
A few additional points:
1. Officers level up, so a level 1 officer is qualified to command a small ship, a level 2 officer can command a small ship squadron, a level 3 officer is qualified for a medium ship, etc.
2. The establishment of space academies produces officers that level up 50% faster, and/or start at a higher level.
3. If a large ship is built without a qualified person to command it (I think level 5 in the example in #1), then that ship suffers a command penalty. It moves slower, gets hit more easily, misses more often. If that ship survives, the commanding officer gets experience 25% faster than normal, as they recieved knowledge more valid to their current post from the battle.
Basically, a randomly generated captain "Honor Harrington" would work her way up the ranks and eventually be a fleet commander.