maybe flagships should have like 3x the hull shield points they have now, so they last longer in that type of game...
So that the player with the surviving flag ship is even more powerful?
Personally i would like to see the damage of bombers upped quite a lot against later ships (2x against cruisers and 4x against caps) but lowered against smaller ships (1/2 against frigates 0x against other fighters and bombers)
Totally imbalanced.
A full bomber squadron already does 5*44.4=222 damage per attack run. With your changes they would do 4*222=888 damage. Since bombers do only 75% damage against capitals, we would still have 666 damage (49.3 dps).
Besides, bombers already do only half damage to everything besides the Kodiak and all buildings.
This would allow us to use fighters tactically by looking/scouting the enemy fleet and building what can hurt him most without swarming with 10+ Perechien.
Spamming Perechians or hangar defenses would then be totally overpowered. Or how about the Sova Carrier? It's also a capital ship which would then be overpowered against other capitals.

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The problem is not how fast or slow capital ships die. The problem is that the player with the surviving flag ship has a lasting advantage. Not only because of the resources the enemy has to invest in to a new capital ship. But also because she has now a higher level flagship.
Imho the solution has to be different, then just to make capital ships weaker.
The capital ships in Sins are basically what the heroes in WarCraft III are. Very powerful units which, when you lose them in the early game, give you a strong disadvantage.
Now if dead heroes in WC3 would have been dead for ever, game play would have been totally screwed up. But that's what basically happens in Sins. A dead capital ship is dead forever. Yes, you can build a new one. But thanks to it's high cost and it's low level, you'll still be at a large disadvantage against the enemy. A lvl 4 or 5 capital ship (which you get very fast with your starting capital) is a very powerful asset.
Now imho Sins should go the same way WC3 did. Make the heroes respawnable. Since we already have crew for the capital ships this wouldn't be to unbelievable. When your lvl 5 flagship gets destroyed, your next flagship of the same type will also be lvl 5 (or one level lower as a penalty.) Of course you could make that even more complicated, with escape pods, time it takes for them to reach home, etc. But it's quite a gameplay issue and imho a solution like this is necessary.