The lacklustre performance of cruiser missiles is due to the cruiser stats themselves, not the pilot nor the stats on the missiles... At least, that is my perception.
A while back, before the deletion of my nice BHG Destroyer, the two missiles with four tertiaries and two inferno's worked quite well on just about everything except a battleship. Of course, I couldn't do the same damage as I could in a gunboat with six guns, but thats not what a destroyer is for. Besides, if persuaded to do some maneuvers, some cruisers can come out on top against a pair of good fighter pilots.
I've actually found that cruisers as they are now work best as light artillery vessels, though long range artillery lies thin on the ground here at disco. Direct combat just isn't where the cruiser class excels at all, which is why in my opinion, they feel underpowered.
Gunboat missiles are indeed very effective. Even against the best pilots who fly non-vanilla ships, they are a real threat. It took three IND fighters to chase away my Corsair gunboat once (left with half a bar of hull T_T) piloted by the cream of the crop. Since that level of concentrated skill lies only in a few factions nowadays, it would not seem unreasonable for the stats as they stand to be capable of taking out, in short order, less skilled pilots on a larger scale. These do deserve a nerf, but I would say make them take even more energy and decrease their rate of fire. I would be against giving capital ship missiles an ammo limit, because capital ships have far more space to store ammunition.
BS missiles do need an upgrade in terms of speed now. As of now, they are only good as a gun screen to confuse your enemy's targetting reticule, not as an actual offensive weapon. Even on their intended targets, fighters, they cannot hope to keep up or score a hit on all but the greenest pilot.
Anyway, thats what I think on the matter....:unsure: