1. Make sure that all the current military starships have a good at ship cap "utility value" (using plasma siege starships and raid starships as examples of military starships with a desirable at ship cap "utility value"), and rebalance lines that seem to be falling short of that goal.
2. Lower the knowledge costs of Mk. II and Mk. III military ships (except for fleet starships, for which their Mk. III and Mk. IV costs would be adjusted, and Riot starships, which have an odd knowledge cost progression and thus need to be considered specially)
Starship Bombers are good at what they do, as they are. That is a Fleet Bomber which is instead a starship.
Bomber I: 98 * 9600 / 12 = 78,400/s dps raw, with 6* bonus against some pretty heavy duty stuff, making that 470,000/s optimal.
Bomber SS I: 4 * 140000 / 2 = 280,000 DPS Raw against anything large enough to hit. No boosters though.
I use Bomber SS a lot against AI Eye worlds and Guardians. I'm not sure they need adjustment as a unit. However, at 5000 K to bring to Tech II (7k more to III), they're not versatile enough to invest in. Particularly not when a Raid SS performs 3x as well for the same general abilities and can hit small ships. Raids at 4k are worth it because of their amazing abilities. High speed, FF ignore, and post killing. They are the goto unit for anti AI Eye worlds except for Spire Shield units.
So that leaves anti-large unit and anti-fortress as the Bomber SS's niche. Does it perform so well at MK II that it is nearly worth the upgrade for Fleet Bomber III? Oh, no. No it doesn't. Abilities are fine, K cost is poor.
With the newly rounded pieces behind the upper level of the fleet starships, I'm not sure I see the K value in them. I've yet to really feel a need for their power, compared to alternatives for the K cost. Particularly since they don't stack once you've gotten to Zenith your other flagships are really just there as backups. They're the fleet support ships. You start with Light, which gives you a 140% boost. Each flagship increase gives you 30% more boost in the fleet, plus a few more guns in the mob (and these ships are usually hunted down and smashed to pieces quickly).
At 2000 K a 30% increase across the fleetball could be valuable.
Another 5000 K for another 30% increase to the fleetball. By ratio, this isn't worth as much. The difference between a 170% boost and a 200% boost is actually best illustrated by example. Bombers from above. A single bomber has an 800 raw dps. At 170% it's 1360/s. At 200% it's 1600/s. A difference of 240 points. That's actually a 17.6% boost to the last damage boost. The 230% increase at 7000 MORE K (not total, MORE) is worth even less.
That's 14000 K to bring the fleet starship line up to full strength. Their primary duty/niche is fleet support. After Flagships, they're just not worth it. 12000 K is two MK III/IV upgrades, worth far more than a mere 25-30% boost after the double upgrade.
Leech: I leave this evaluation in the hands of someone who actually uses parasites. They're filler in my fleet.
Plasma Bombards: Small ship eradicators. If it hides under forcefields it beats them to pieces, if they're free-floating it shuts their engines down. In small packs quite useful. However, are they worth the 5/7k price tag to bring up to higher levels? Not to me, unless I'm playing with odd tactics. The ff killer ability isn't that powerful because I never use these alone or in small fleets. They automatically fire up alerts all over the place being a starship. Thus, if I'm going after a system, I can usually lay waste to any forcefield causing me problems, whacking the little guys underneath is just a bonus. In the early game this can be a boon, since your fleet vs. ff power is usually weak, but that's for the MK Is. In the mid-late game the upgrades are not worth the K.
Cloakers: I've never required the ability to cloak more than 40 ships at once. My raids are very small in unit # under most circumstances. However, at a whole 2000 K to cloak 700 more ships, I think they're priced well if you use that tactic heavily. I just never need to.
Neinzul Enclave Starship: Okay, I'll buy the 10,000 K price tag on the MK IV, merely because it allows you to circumvent, permanently, the loss of a MK IV factory, but that's if I could directly buy it bypassing the lower levels. 3000 K and 5000 K for the II/III seems silly to me, particularly with how fragile they are. These need an end to end overhaul in general though, from my perspective, particularly due to the necessity of Engineer IIIs to make them useful in any type of scenario where you're not on your own controlled worlds, in which case you could simply fire up a Space Dock.
Riot Starships: I think everyone knows of my love affair with the MK II Riot Tazer. At 4000 K I feel that bonus is priced about right. It's expensive, and it should be for the defensive power it gains you. However, at 5000 K I don't see how the Riot III is priced. I don't, however, use these utility ships in standard techniques. I'm not an 'engine killing' kind of guy. For the price, I don't want to kill an engine, I want to kill a ship. At 5000 K this Engine Killer is worth 2 MK II upgrades. It needs more utility. Tachyon sweepers like the decloaker, A tazer AND a tractor, so it feels like you've actually upgraded from MK I, something... I dunno.
Scouts: Just got an overhaul, no opinion until further heavy usage. Right now Scout Is are doing what I want/need, with the inclusion of the Brave Scout SS addition.