well, yes - there is certainly a way ( or many ways ) that could balance the ships much much better, no doubt about that. - but i am not sure how much work that would involve or totally redefine the mod as such. a minor change will only do so much though. ( like increasing the projectile speed on energy weapons is the only thing that might not have a greater impact on the balance, cause in a fighter vs. figher fight, it might do the trick - when a fighter fights vs. a gunboat or bigger, i don t think the fighter hits much more, cause the hit ratio is quite high anyway vs. big targets.
increasing the raw hull / shield damage of weapons can have a negative effect on the capital ships. fighters aren t exactly weak when they are deployed in larger numbers ( 6+ ). yet they are allmost unstoppable by a capital ship ( the mighty checkmate move ) ... i really don t know what effect it would do - but i can imagine capital ships being simply outclassed.
one might think that its OK to take down a battleship with 6 fighters - ( sure, why not ) but even in a teamfight ( which is considerable harder for the capital ship, cause the captain gotto make sure that his fire doesn t hit teammates ) those big targets would go down even quicker than they do now.
so out of all the suggestions - only the increased projectile speed sounds like a good thing that might not mess up the precious balance towards other classes too much. ok, less bats/bots helps, too - but maybe the NPC encounters have to be rebalanced then - 1 bomber vs. 5 battleships ( npc task ) with half the bots/bats might be interesting... .
but here is another aproach towards the original problem. maybe it is possible to attach the shield regeneration to the energybar - and that means, a lot more than now. so maybe - in order to regen the shields from ZERO to 25% ( i think its 25 or 20% ) it would take 70% energy. ( you d have to have the energy available + its gone once the shields replenish ) - so fighters would stay without shields longer than now ( while they dodge some and regain some shield back ) - they can still dodge, but their ability to fight back is crippled - and the chance that they are shieldless is greater.