The Vanilla ship imbalance, in my opinion, should be solved by the removal of the wireframes. Of course if it cannot be done... The one issue is that the ships will lose the "falling apart" effect from Vanilla, and that was pretty cool. So, question is: Balance or Style?
Fights takeing too long? Well just decreasing the ammount of armour on the ships seems the most logical... increasing the damage may work, but incraesing it on the fighter (lower) end may make others demand an increase all the way up. It is easier to decrease the stats on the lower (fighter) end... Projectile speed; the only other stat I can see this being directly compared is the fighter agility (or the armour on fighters with a determined agility stat). Now, because agility is not easily determined, I feel the projectile speed is kinda arbitrary if your not just balanceing the guns against each other. Decreasing armour seems the most logical, though the insta kill weapons issues may be complained about some more after...
Bomber armour. I have always thought it seemed ridiculous that bombers had such advantagous armour. How often does a bomber actually get hit by a Capship? How different is that to a regular VHF? Bombers are just VHF with a much better power supply and the ability to capitalize on it. The armour is just another advantage. My suggestion is to have the armour on a given bomber equal to the armour on the VHF that has the same "agility" as the bomber. Don't know if this is already the case or not...