TL;DR version: Human Fortresses, minor to moderate tweaks. AI Fortresses: Nerf the basic unit, reduce the level of hard counter, give it a weaker ability to interact beyond just the range of the main guns.
From my thread earlier, I came to change how I view the issue. The way I see it now is there are at least four potential overlapping roles, some existing, some not.
1). Territorial control. Putting a fortress up in a minor border system or as a beachhead in hostile territory. Range, durability are key. This is the most common role for the AI as well.
2). Heavy Weapons Platform. Putting multiple fortresses in one world to output maximum firepower. Their abilities aren't nearly as important as their firepower/cost ratio.
3). "Stronghold/Base". Establishing a fortress as the center of the operation. Competing for knowledge with Mobile Repair Stations, just one provides strong but not gamechanging support. Range isn't so much of a concern as their ability to be up front with the fleet, supporting it with fire, repair.
4). Modular, customizable
5). AI owned obstacle. Sometimes, even without a fortress AI, they show up in just the right place to actually be interesting. Other times placement just influences the order you choose targets.
Since this isn't a brainstorming session, I won't go in depth into some of the abilities, but I will give some brief examples to give context to the above.
A). One of the suggestions involved tweaking the costs and stats. This would not affect the basic desire for fortresses to fill other roles or be 'more interesting'. Its primary concern is role 2. Particular concern should be paid to its effects on role 5
B). A second suggestion involved turning them into some sort of command and control center, as well as giving them drones. Drones with a long enough range and quick spawning could be an interesting factor in AI systems, as they would effect the entire system. They would function well enough in role 1, but likely fail role 2. They could easily be balanced at lower cost/power but higher cap.
It seems player concerns factor into three very broad categories: I like their role but (might) want to adjust their balance; I want a different role entirely for us humans to play around with; I'm more concerned about how they fill out the AI's role, want to make them a more interesting obstacle.
I like their player role, but want to adjust their balance or tweak to make a bit more engaging to use.
I wouldn't mind another line of 'Strongholds' fulfilling a less expensive role, combining basic system functions (stardocks, supply, energy collector), that is significantly weaker and less expensive, but comes with (no shields) but interceptor/bomber/slicer modules from the champion line (yet with neinzul-level attrition). This would fulfill a more support and counter role, able to handle a wide variety of loose AI ships at any range, but at a very small, non-wave capacity.
I think in AI hands they occasionally provide a very interesting challenge, but in most cases merely result in detours. If it placement was improved or replaced with an alternative when an interesting location was not available, it would make taking down defensive AIs interesting, as well as requiring alternate techniques to clear. We already have various neinzul clusters, something halfway between those and existing fortresses would be a compromise.
With regards to the upcoming release, I'm not really interested in a massive redesign of player fortresses. The current system is not broken, and has decent balance. That said, the idea of redesigning AI Fortresses to make them (a)less of a hard counter (b)more flexible, capable of supporting beyond just the denial range of their guns is something I'd be for.