Is now a good time to mention my idea for a Carrier Starship? It's a slow moving starship that can manufacture fighters and bombers (although not as quickly as a space dock), it also slowly repairs fighters/bombers in a certain radius around it.
It should look like the Battlestar Galactica. It's fighters should look like Vipers, and bombers like Raptors. And, of course, it needs to run on tillium...
Okay, but then there has to be a, 'Cylon', AI Type that exclusively deploys base-stars and teleport-raiders. Also, the Command Station fog-horn becomes a 'Frack!' sound.
With regards to leveling up, maybe just the starships should gain experience? As you say, the smaller ships tend to die too quickly.
Additionally, what about environmental hazards? for example certain systems could be nebulae that render scouts ineffective or asteroid belts that slowly whittle down ship's hp as they pass through them.