A thought struck as another alternative for 'balancing' from your post. Raise the damage of pulse and other shieldbusting weapons, but also raise the shield strength of transports, gunboats, cruisers and battleships. At this point, once you grind down the shield it is effectively useless as a single SNAC will bring it back down and allow for the pilot's companions to unleash once more. However, this would then bring in balancing issues where small numbers are concerned. Perhaps lowering the regen value?
Bah. I stand by my point. Theoretical balancing is much too fiddly.
Edit - Very good! You've found a flaw in my argument, and taken a broad statement as a personal offense! Congratulations! You will find, however, that in the case of gunboats and fighters, you can once more push the limits to extremes with your skill, and I believe far more so in a gunship/gunboat than a bomber. The satire in that statement was directed at Tenacity, as he said something similar directed at bomber jocks.