I think by this point it's basically established that they're going to stay worthless for a while. The best choice is to use siege capitals or simply not play the game.
In classic developer over-reaction format, they nerfed them so badly that it actually became more cost effective to just build siege capital ships rather than siege frigates. Oops. So Ironclad was in such a frenzy to correct the perceived “imbalance” they neglected (or at least, made a decision) to make the unit so inefficient from a cost perspective it becomes near-obsolete.
