Just chiming in that fortresses are an (almost) must have for me.
Mk Is are unlocked by mid game and Mk IIs quite often as I move to late game.
However, this is due to my defensive setup. I play realistic or lattice maps so my border worlds commonly have 3+ hostile warp points.
I had a whipping boy system with 8 hostile wormholes a couple games ago.
I can't built turrets at every hostile warp point so the majority of my defenses sit around my command station. I park a fort there so it's repair beams are in range of most of the turrets in the system.
Park some grav turrets about the system and things just die.
The down side is there is no second chance. In a warp point defence you have some time between going "my defences won't hold" to "command station under attack" to bring in your mobile ships.
With all the defences at the command station, you only have seconds and the command station can just outright die if there are FF immune units about.
I suppose what I'm trying to say is my defences are built around the fortress, especially because of it's repair beams.
I can't argue with the firepower either of course.
edit: Just had a thought, right now fortresses and golems overlap for the 'superweapon' role. What about changing the fortresses role to 'make this system survive'.
By this I mean make it so that it gives the players command station invincibility while alive? (With appropriate tweaks to it's DPS and Health.) I don't know how other people run their setups but I reasonably often have my fortress still alive even though my command station is dead in the system.