So I've run a couple campaigns at this point and wanted to share some thoughts on the colony side of things. A number of ideas have already been expressed by others here on the forums, but I'm going to try to synthesize an overall game design concept. With the caveat, I don't know what the plans are for end game, which might render some of this moot.
It appears to me, players like to be rewarded, and dislike being punished or at least the appearance of punishment, for what should be gameplay progressing actions. Going out and exploring should reward the player in some way. Spending time and credits on colonies should reward the player in some way.
What are the possible exploration and colony playstyles?
For exploration, which can be mixed between the two:
1) Go explore and sell everything for credits and skip colonization. Do the gameplay, get credits, spend credits on a better fleet, and done.
2) Go explore, find colony system(s), find planet improving items, colonize with said items. Gain the benefits of a place to store your stuff, as well as credits and building ships to improve your fleet.
The first style is somewhat bland, although more interesting than straight up trading. I would like to suggest to improve the first option, and perhaps make it more appealing while making all those spare exploration items more useful than just plain credits, is that having an option in addition to just selling, treat them more like cores. Make it so you can interact with a faction planetary governor or commander, just like with cores, and that the player can get credits, reputation, or perhaps a potential contact if sufficiently valuable (like a Pristine Nanoforge for example) that way, and the item gets sent to a faction world that can actually benefit, if possible. Although probably only one contact via this method per faction, otherwise you might "give" it to them, raid for it, and "give" it to them again. If a planet killer device can get you a very high contact, why shouldn't handing a Pristine Nanoforge to the Diktat (for example) not do something similar?
When doing the second style, having a found a colony item and being simply unable to use it or seeing the penalty for using it feels worse than not using it, feels bad from a player perspective, even if it potentially gives more overall benefit than the negative (hostile activity tracker penalties). You get the positive hit of having found something rare, and then the realization, that what could have been valuable is just some spare credits. So this gets more deeply into the Hostile Activity tracker and colonization styles.
Colonization styles:
Case 1: Player doesn't interact with the system at all. They don't create colonies.
Case 2: Player just colonies randomly a single or few planets as way points, and lets them grow naturally without any heavy investment. Perhaps builds and abandons techmining outposts.
Case 3: Player stays within human administrator limits and keeps each colony off the Pather's hit list (i.e. under the 7 or 8 Pather interest) or at least keeps it under what they can offset with bonuses.
Case 4: Empire builder who finds the right system and just colonies all the planets with alpha core administrators and every single item they've found. Either they eat the tracker penalties or use the quest options to eliminate them.
I would step back, and ask what should the game reward the player for doing? Should the player who goes out and grabs all the alpha cores and explores the entire sector have better colonies than the player who just avoids Pather interest and simply doesn't interact much with the system? If so, then how can we have the system provide a clear reward.
My suggestion would be to make Military Bases and High Command even more expensive to maintain but let them stack for the Hostile Tracker (and potentially new trackers). Make the decision be either live with access and stability penalties from the hostile tracker(s) or go full on military powerhouse and instead of having penalties reducing monthly revenue have higher monthly credit costs. Which gives incentive to the empire builder to be fully self-sufficient, cutting potential military base upkeep costs by half. Also makes low hazard worlds more attractive from a defense perspective. So instead of having a size 6 High command cost 28,000 per month, make it more like 280,000. Bump a size 6 Military base up from 20,000 to 200,000. Or something like that, the exact numbers need playtest. Make it so you need a full economy behind it, and the opportunity cost not be just a single economic industry being missing, but essentially take the slot and cost the profit of a second economy building to maintain as well. Increase the net cost to build the High Command to a million or two. It is easy enough to argue that sustaining a military to rival the Hegemony should be really, really expensive. On the other hand, if you are sustaining a military to rival the Hegemony in a single system, you shouldn't have any problems with Pirate or Pather fleets.
So instead of have some kind of interaction with Pathers like the Planet Killer quest, you also could let your actions and colony choices speak for you. Millions for defense, but not one cent in tribute.
So working backwards from how much you'd like to see an end game colony setup making in profit, I'd suggest adjusting industry and military slot costs for building, upgrading, and maintenance, based on the various potential setups. Pather interest under the radar, so hostile activity tracker stays low, but industries make less. Perhaps a single high command in such a setup to handle pirates supported from 4 human administer colonies. Huge investment into cores and colony items, but going all industry and minimal military to just maximize raw credits and just accept the accessibility penalties and attack fleets. Huge investment into cores and colony items, but also a huge expenditure on the military which reduces overall profits (in the same way accessibility and stability penalties affect profits), but feels more like the player has agency, even if the end profits are essentially the same, or maybe even less than eating the penalties option.
I would also suggest letting the Military Base upgrade to different specialization options. Imagine instead of just a High Command, you could also pick something like Internal Security Headquarters, which gives less help to Pirates, but much more effective against Pather Cells and Pather interest. Maybe also stronger against Tri-tach. Or a Merchant Marine Hub which increases the military strength of any trade fleet that either leaves or goes towards your faction's colonies, or perhaps just flatly reduces the penalties for destroyed trade fleets on the colony. Also being stronger against Pirates, but less effective against Pathers. High command could be stronger against more traditional faction hostile activity trackers like the Hegemony or Diktat.
This way if you make a deal with Kanta, you could specialize towards focusing on Pathers. Or vice versa. And if you don't want to kneel to either, then be a stander and pay a million credits per month to have the strongest military in the sector. Install all the Alpha cores and build all the Internal Security bases and have a dystopian society where non-human AI cores are always looking over your shoulder, rooting out Pather dissidents (and perhaps any threats to the AI themselves). Your very own AI run Diktat.
I think long term, splitting the Hostile Activity Tracker into different independent trackers makes sense, allowing for the possibility of clear reputational interactions. I'd suggest a tracker for each faction would be the way to go, which is also influenced by the various reputation. If you're sitting at -25 (suspicious), I think a faction should be more willing to send clandestine raids than if you're sitting at +80 cooperative, which could be a montly plus or minus on such a tracker. You could also have the tracker take into account cross reputations. If Tri-tach is at war with Hegemony, and you're at a high reputation with Hegemony, then a Hostile Activity tracker for Tri-tach could be growing faster because of "ally of my enemy", which might be partially offset somewhat by a smaller "my ally" bonus since you might also have high Tri-tach reputation. Commissions could also play a factor in the trackers. Same goes with Pirate and Pather reputations. This would naturally make being allied with the Pirates a negative as essentially all the major factions would have an inherent hostility tracker increase all the time since you'd be an "ally of my enemy". Maybe a bonus "ally of pirates" increase as well.
If you go this route, a link to related hostile activity tracker from the Faction screen would be nice.