I don't know what you're talking about with b'rels outgunning Akiras or most fed ships for that matter. If you're using the b'rels then how much research did you have vs your opponent? The Akira will stop a b'rel dead in the first torp volley, and if the first one doesn't get them then as it moves behind the Akira the aft volley will. If you're still having trouble with the BoPs then exploit their weakness. They can only fire forward so...
As for torpedo damage, we kinda got tired of watching a ship eat 20-30 torps and barely have a scratch.
2: Feds Hanger defense does not have an option to spawn fighters of bombers
That's on purpose.
After my first game, my initial reaction is that capital ships in general may be a bit overpowered. A Galaxy and a Nebula by themselves took out the entire pirate base full of Dominon ships without either of their shields going below 50%. I like that they're heavy hitters, but they might be a little too powerful at the moment.
If you had the galaxy and nebula then you probably had a fair amount of the research. On the other hand those were totally un-upgraded ships in the pirate base. If they had full research I'd place bets on the dominion.