A few more observations.
I agree about not having the A.I. always do the same thing, even if it looks like the optimal route. Predictability just means death against any human player.
I had no clue that Guardians were essentially self-defending slow but mobile carriers. Their behavior makes a lot more sense now, but you might want to somehow make this point clearer.
Slowing down building static structures during A.I. presence makes sense to solve the "bouncing target" problem, but it also makes turrets and tractors even weaker than what they are now. Given the numbers the A.I. is currently throwing around, you might not even bother building them.
The thing is: as soon as the A.I. has enough units to manage even a few escape from tractor beams, your turrets are nearly instantly lost. What's the point of having even 50-60 of them if the A.I. routinely attacks you with hundreds (and later thousands) of squads? There are simply way too many targets for them to inflict significant damage before getting destroyed.
The "rebuilding target" problem solves this by "forcing" the A.I. to split its forces, make them a lot less effective, and allow for the controller to rebuild fast enough to let the turrets inflict significant damage over time, but it does it in a perverse way which makes the A.I. look dumb.
For me, the best solution to the "scrap and rebuild somewhere else" problem is to allow fast travel. If I want to rebuild somewhere else, it's because I'm attacking planet X and the A.I. is attacking me on planet Y. And given how fast A.I. waves are, that's basically a constant situation. It becomes fairly frustrating because, as I said, it feels like a protracted game of whack-a-mole. My thought during that is "God, how much more time do I need to waste chasing these stupid A.I. waves".
The alternative is to allow for fleet-wide ship caps (in addition to the galaxy-wide ones) to make multi-fleet operations manageable for a human player.
And now for a few more test results.
I tried another quick game, this time at difficulty 7, and around the 40-60 minutes mark the A.I. just starts sending in ever-escalating waves that overwhelm me (even if the AIP is not growing anymore, as I'm busy trying to survive rather than conquer new planets). They're so big (comparatively) that it takes longer to clear them than it takes it to send the next wave, at which point the game is lost.
I was starting to think the A.I. is seriously overtuned right now, so I did another test at default settings. I just built the starting fleet and a defense at my home planet, and let it run for 40 minutes or so. I got a few incoming waves all at strength 260, but it looked like the game was behaving correctly. Then I conquered one planet and things started getting weird. For one, as soon as the ark moved, I got the cross-planet attack notification and threat jumped from 0 to 3500+. I'm assuming it's the activation of the hunter fleet there, but after conquering the planet and sitting there a bit (savegame 1), if you click on Troria (the nearby Mark I planet) you can see Mark IV and V ships, which should not be possible (I think..?) on a Mark I planet at AIP 30.
Then things started getting even more weird. I've attached a second save game where there's a 980 strength wave attacking (from 260 to 980 with just one planet?). The wave will charge then run to Troria without engaging. Wait for them to be gone, then move the fleet (without the Ark) on Troria, let it sit on the wormhole, and look what happens in the next 3 minutes. Something is very wrong, I think.