Mark III Fleetship - As mentioned in another thread, their K cost is prohibitive. Compared to Starships, they require a much higher constant economic drain due to attrition. They also take more user micro to get replacements back in position.
Raid Starships - Besides the wacky K costs, they really need utility when upgraded rather than combat power. Otherwise nothing short of an absurd K-cost will make them attractive.
Station Upgrades - Aside from Military III (purely on a choke world) these need help. It would be much better to have much lower caps. Single cap for Mark III, 2-4 for Mark II, and give them some real punch.
Turrets in General - These are almost always a bad buy because they at best cancel out the AIP from expansion on the defensive side of things, but you still need to deal with reinforcements. So until you hit the reinforcement cap, these just aren't super great. I'm half tempted to say nerf all turrets, but bring down their upgrade costs so we can effectively upgrade them to get the same level of defense. Currently in 9/9, Mark Is are fine for the entire game. I'd even say go as far as add Mark IV turrets.
Engineer III - Maybe K is too high, but the biggest change I want to see is make them immune to reclamation. It is far to easy to Reclaim AI Engineer IIIs so you never need to unlock them. Find a Mark IV world, kill everything except the command station, and far the Engineer IIIs that spawn there with Leech Starships.
Zenith Space Time Manipulator I've never used, so I can't comment on.