I don't know about anyone else but the Zenith starship and the Spire starship just seem too costly knowledge wise and just don't seem that impressive for the human players. I never ever research these ships as i would rather spend the knowledge on a MK III fleet ship or two instead. I would rather get the damage boost from more ships than a very costly starship that doesn't do much damage really.
Yea, I would agree that their "rebalance" sort of nerfed them rather than helped them. In fact, as I have mentioned many times before, K costs for military starships are too high in general compared to fleet ships. I'd say, either rebalance the military starships overall (using the plasma seige and the raid starships as guidelines for good Mk. I starship usability), and review their knowledge costs for Mk. II and Mk. III versions.
As for the Zenith and Spire starships, I don't really think they can be truly fixed until they are split into their own lines (aka, a fleet starship line, a zenith starship line, and a spire starship line) which can be balanced individually and be given their own "personality", sort of like what they had before, but not locked to higher tiers (and thus higher knowledge costs)
EDIT: In fact, can I nominate military starships (with the previously mentioned exceptions of plasma seige and raid) overall? And also nominate all military Mk. II (except for fleet ship Mk. II) and Mk. III military starships?