In a different thread, I had an idea as a potential solution to the problem of Arks being too mobile that after thinking about it I decided would probably be pretty cool whether not it is used as a solution to that, so I will copy and paste my comment, any possible follow-up comments I may have forgotten about, and though some of it wouldn't really apply here, the rest might work.
I haven't gotten the alpha access, so I don't know exactly how things are now, but I am not fond of the idea of a punishment for moving your Ark, especially since you have to move it for hacking and the such, and I like the idea of being able to use it as a powerful unit for attacking, but with a high risk and losing out somewhere else. Maybe a solution could be something like having it provide a lot of resources, and if you move it off a planet it "disconnects" from the grid, and makes no resources until you have it on a planet for so long until you can reconnect it. Alternatively, maybe have something where it is too big too fit into wormholes, or has extremely advanced weaponry and shields and the such that unfortunately don't mix well with the wormhole, so you have to build a special structure on the planet it is on and any planet you want to move it to (and a way to build one on hostile planets), allowing it to get from one place to the other, and if you move it somewhere vulnerable, the AI may try destroying the structure in order to cut off any retreat until you can rebuild it. The structures could also work as something needed for stuff such as golems as well. Maybe have an alternative option to be able to disable all functions besides movement to get rid of the interference, allowing it to move to other planets, but with all the systems taking a while to get back online, possibly including a sort of cloaking device that only protects from scanners, so unless the AI is on a planet with it they won't know where it is, but if you choose that option to move it rather than building the structure it pretty much tells the AI "Hey, big juicy Ark here for you, if you think you can destroy it here." That could also possibly be further complicated by having various systems and the such doing different tasks, such as resource production, manufacturing, shields, engines, weaponry, and the protection from scanners, and if you go through a wormhole without using the special structure you have to choose some to disable, and possibly have it where you can increase power to each system normally at the cost of decreasing the power in another, for example, if you are fighting you could redirect all power going to scanner protection (since the AI already knows where it is) and resource production, so you can increase power in your weapons and shields, or when you think you are safe, you can do the opposite, though of course it wouldn't be instant.
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Actually, even if not as a solution to too much mobility for your ark, I think having different systems and the such you could adjust the amount of power going to in order to specialize the Ark for a specific purpose at the moment would really be a pretty cool addition, to prevent using that kind of stuff as part of balancing mobility from causing issues in the early game, since you are supposed to be able to choose a planet to take over as your homeworld that you have to fight for, maybe you could have it where until you take that first planet the AI won't realize the Ark is a threat or at all important and won't care too much about it besides having ships on the planet attack it, or maybe have how much priority the AI puts on it as a target be dependent on your AIP, when it is low, the AI doesn't consider the Ark or us puny remnants of human resistance a threat or anything worth paying attention to, but as it goes up, they care more and also notice more and more how often you use the Ark, and at first suspect and later be certain that it is key to your battle against them, and therefore an extremely high priority target.
There a few different things I think would be cool mods in there, the structures needed for Ark and golems and the such, the different power systems in the Ark and maybe the system I thought of to have that work, and the thing where the AI only realizes the Ark is a threat or that it is important as your AIP goes up and they have the chance to see it in action and see what it does.
