EDIT: Just a thought, but I think I'm leaning to Forts being tough but less DPS monsters. So their supposed to hold the line while other stuff does the killing, rather than do it all themselves. I think the AI Fort has closer to the right toughness, and maybe light engine damage might be appropriate (similar to Riot SS with a cap on engine%, but less actual ED/second). Just enough to slow stuff down while your fleet in to deal with things.
Without major DPS how would they "hold the line"? Kirrahe style?
More seriously, the only thing that comes to mind is to have them emit a forcefield and/or have tractor beams and/or grav effect, etc. Or do you think the Riot Control Fortress effect would be sufficient?
First, bring their health up to AI Fort levels. 60 million hp for Mark I. Then bump their armor up. Somewhere around 10k-25k per mark. That's enough that armor piercing ships actually matter against them, and ships with incidental armor piercing (Fighters, for example) don't ignore their armor. Then give them the ED effect from Riots with "cannot reduce below 25%" and maybe 20 ED/mark. With their huge range, that's a pretty potent ability to slow down any attacking force. I honestly would probably also consider giving them radar dampening. Finally drop their damage by 75-80% and change the polycrystal multiplier to 0.5.
I'd consider that a reasonable first try at roadblock-style Fortress. I think some other defensive effects might help if needed, but those might require new stuff. Like maybe it could have a chance to paralysis for 2 seconds, or maybe just a plain 1 second paralyze.
I find the EYE's combined with the new GPs much more annoying then Forts. You already have to bring in a greatly reduced assault force, and ontop of that the GP will have easy work dealing with the limited numbers of whatever you send at them. Forts also are semi rare and many times can be ignored mostly, however you need to kill all GPs to take out EYEs, or to take over a system. Maybe introducing a 1-10 setting for GPs would solve a lot of the problems (shouldn't be too difficult hopefully?) and while we are at it have Raid starships a 1-10 or easy/med/hard. One of the things I love so much about AI is how customizable it is to different playstyles.
I find a lot of people give Eyes too much weight. With the exception of Nuclear Eyes and Core Eyes, I basically ignore them all. They have an effect certainly, but most of the time they are tricking you into sending in too small a force. Say I have 600 ships and the AI has 200 in a system with an Eye. If I send in my ships use right-click targeting to take down all the critical targets, at worst the Eye will trigger until I've lost 200 ships. I can normally kill all Guard Posts near the entry warp point and retreat losing at most half my force. That gives me a safe beach head to get in next time, I haven't killed any of the AI ships so I still can fit 400 ships in without triggering it. Often my second raid barely triggers the Eye.
You can also hilariously cheese Parasite Eyes if you have high cap ships, although its really more work than I consider worth it. Because the AI generally has higher Mark ships than you, what you do is go in with a bunch of Mark I high cap ships and your Fighters. You goal is to kill the higher Mark AI ships and let the AI replace them with your Mark I units. Then go in as above targeting only Guard Posts and what have you, but now you are only taking DPS from weak Mark I ships, and you aren't even triggering the Eye at all.