The original implementation actually felt about right for the player, although I didn't have to fight against them in any of my games. A pair of frigates would deal serious damage to incoming waves and were pretty useful on offense too - being able to warp in, defend a perimeter around the wormhole, and snipe down guard posts/special forces posts was a nice alternative to neutering planets with <insert mobile ship here> (almost always raid starships.) They were almost a subcompact starship and felt nice and unique, but now are too expensive energy-wise and too weak. The AI will have counter-sniper turrets up before they can take much of anything out on offense, and their effect on defensive battles is too slight to even be noticed.
For the player, though, the original concept was that they be powerful enough that the player had to make careful decisions about where to deploy the limited numbers available - again, sort of like the starship decision space, but with higher caps and the interference penalty so that "all in one spot" was out of the question and it was more an issue of coverage. So, in keeping with that my suggestion would be to return them to something like their original power and lower the caps. Actually, I think scaling the cap by the size of the galaxy would be the best choice, if that's possible implementation-wise: maybe one frigate per 7/8/9/10 planets at mks I-IV or something similar.
I'm not sure how to deal with the issue of how the AI uses them. Do all ships have to be available for use by the AI? Maybe this one ought to be humans-only.