Sometimes I have the feeling people mean something very different than I do when they say brainstorming. Let me be clear: the following is not a suggestion or proposed change, and I'm fully aware of the in-feasibility of it all. It was fun to think of though. I do have a more modest proposal, but I thought I'd lead with the insane one since "brainstorm" is in the title.
Operation Triple the Work:
Branch Fortresses into three distinct lines, all of which are available.
Modular MicroFortress: Five times the cap of a regular fortress, a tenth the firepower, a tenth the cost, and a fifth the health, and no repair beams. You can anchor up to three of them on a wormhole or asteroid. They get one support module such as; Gravity Drain; Sniper Railgun, Shield Buster (single target, large targets only, decent damage, bonus to structural/heavy), Spider Cluster, Paralyzer.
Stronghold: Similar to Warp Jammer Command Stations, you have a total cap of six, and it can be built in place of a regular command station. It integrate a single fixed radius modular shield that costs resources to repair. Alternatively, it can carry one long range missile similar to an AI missile post, to take care of stragglers, while technically not being a sniper weapon. It integrates several normal system functions by integrating Stardocks, Starship Constructors, neinzul regeneration, and energy collection (prohibiting one from being built in system, stronghold produces 50k energy). It does not have a repair beam, but it does have a significant amount of weaponry, roughly equivalent to half a cap of the MKI Frigates, Fighters, and Bombers. The range of its weaponry is only enough to return fire on missile frigates, taking the shield radius into account. This is designed to more self-sufficient than actually change the results of an incoming wave. Provides supply normally.
Fortress: Damage, Health, and Cost are reduced by a third. They get one heavy weapon module consisting of either a short range ion cannon, mini orbital mass driver, implosion burst attack (short range AoE) or gravity artillery.
A more modest proposal
Drone Support. Fortresses receive three modular launch bays for long range interceptors/bombers/slicers. In return, the human version gets reduce range. Flamewave damage is reduced to compensate. Health is reduced to compensate for the meatshield effect. Entire unit is rebalanced to require less of a hard counter, since the drone modules will counter various parts of the basic triangle. Will provide supply to only its own system.