Edited June 2nd, with more stuff.
Some Feedback about observed behavior.
Some of this could be coincidence. Its just observation. I have no correlations.
I'll keep this one post as a running thread with all I find.
Some of this has already been commented on in the comments section.

1. Guilli's Ship Components must come after StartTech AI otherwise the additional slots and components do not show up.
   
2. Empires now seem to go out of their way to block neighboring empires from expanding by sending a science ship and construction ship to the closest choke point right up against the neighbors territory. They all do it now. The effect creates these pockets of unclaimed systems in between that neither empire can reach since they close their borders.
   
3. Weak AI empires that would normally be asking for protectorate status from the big nice empires now offer tribute instead. Whether they can pay for it or not. Probably a side effect to wanting to expand more.
   
4. Neighboring hostile empires now excessively claim territory deep within your borders. I say excessively because I have never noticed any one empire ever spend that much on so many claims. There is one empire that has over 25 claims and I know they never scanned those systems. They wont stop claiming either. Once they earn enough influence they go at it again.
   I cant tell if its just the belligerent/hostile empires yet, since my other cooperative neighbors have not done this.
   
5. A side effect now of the excessive claims is treaty flip flopping. By mid game I'll have an excessive number of empires forming some treaty with another empire only to turn around and exit the treaty immediately. I say its claims based, because what I am noticing is once a treaty is up, and the other member see's the full territory you got, they make claim for it. Doh. Then the treaty gets broken.
   
6. Almost every empire in my game is at equivalent stage to each other in terms of research. Which is weird. I purposely start up a research federation and invite like minded empires so that we get an edge over everyone else in this department. The research fed is quite OP with tech but comes with some hard to keep parameters for cohesion as the balance.
   Mid game, as expected, I am already at level 4 of the fed, doing repeatables but other empires are equivalent to my fed members. So the research federation seems to loose its advantage now and all you have are tougher federation cohesion.
   
7. I noticed every single non spiritualist empire with organic pops went synthetic evolution. 14 AI Map. I have no correlation other than the hard drive to science. Seems weird.
   
8. A.I. does not build admin buildings. Instead they'll plaster their worlds with research labs to compensate. The author states that is normal and they should start building admin buildings after they get 300 research up. But they will evaluate the value of either a research building or admin building giving they better research points. Seems weird to me, but I get the math and why it happens now.

Edited June 22nd, with more stuff.

I'd like to expand on my observations on claims and war:

I noted above that I saw excessive claims.
Its now past mid point of my game and every 15 or so years there is another war somewhere over claims.
Literally you know you are about to get into a war, when across the top of your screen 10-15 new claims on your territory show up all at once, then next thing you know there is a war declaration.

@Salvor, I know you mentioned you didnt or cant change the claims system and its whatever is in vanilla doing that, but I suspect some combination from the mod has influenced this.
I thought the first two wars before 2270 were cool. Now its getting annoying being in a new war every 15 or so years over claimed territory.

All empires are either belligerent policy or expansionist.
The only empire not giving me any grief is an isolationist empire.

I'm kinda hoping there is something in the mod I can tweak to make the AI's a bit more patient.

I launched an AI only game just to observe how things went with this mod. I kept "Starnet Friendly Patch" but I don't know if that has any effect or not.

1/ In 2280 one AI has 4k tech research, around 100K fleet power and 900 fleet cap (but only use 600, see below). It is WAY above the other AI (1k teach for the second, and 100K but at 100% fleet cap). The snowball can be explained by early conquest which leads to double the planets and pop (althought it purges conquered pop, but as robot they can just settle anywhere and grow). I noticed that in this game robot empire far outshined bio empire.

2/ For some reason this AI never built above 650 fleet capacity although its max was at around 900. Other AI used their full naval capacity and this one definitely had the ressources needed to do so, which let me wondering why it stopped at just 60% of its naval capacity.

3/ When at war, this AI only build its ship in one starbase although it had like 4 starbase with shipyard. And the starbase chose to build was the farest away from the front line.

4/ The 2nd and 3rd point leads to the AI struggling way more that it should against the Fallen Empire in 2300. If it had build at 100% fleet cap it would have managed way better. And the slow build in just one station slowed down the replacement of lost ships. It still won though, despite both AI being really stupid at strategy (but that is a whole another issue)

5/ Despite Fallen Empire Wreckages being litterally everywhere in this AI borders, the Scientist Ships stayed stubbornely "Assisting Science" above worlds and never went to salvage the wreckage and acquire those juicy Fallen Technologies. I don't know if it was waiting for the end of war to do so as I stopped the experiment before the proper conclusion of the war.

5/ I'm now terrified to play this mod considering how much that AI snowballed way better that I ever did.

@Kaery Sen'nin

Unfortunately the problems you mentioned can't be fixed by mods. I have no way to issue scan debris orders, I have no way to queue ships from the mod, etc.

Fallen Empires and Settings

I've notice in several games now, FE's/AE's present zero problems for myself and any AI.
By the time they awaken or if they all of a sudden go to war over say a holy planet, they are just annihilated.

So I made a test. I played a game with 5 FE's and elevated end game crisis strength to 1.75
Still the FE's fell (around 2400) and since a war in heaven was probably the planned end game crisis, it never happened.
I think its the fact the AI's are always trying to expand, even end game.
So the FE's never really get a chance to spin up a threat to the AI's. I suspect upping the crisis strength might not even help here.

The games seem to go something like this:

FE: You AI empires will be squashed like bugs
AI: Whatever
FE: Stay away from the holy worlds.
AI: Those are some nice looking GAIA planets you got there.
FE: I will awaken and begin too ...
AI: Say hello to my 1.5M fleet power and advanced weapons I've been researching exclusively for the past 100 years.
AE: Wait what?

Any way to give more of an advantage to these guys to make them a challenge?

So, I have an idea for how to make the "truce timer" configurable. But first, some information:

Planetary Diversity opens a menue at the start that allows you to select something involving habbitible worlds. Not sure what it does specificly, but still...

Giga-structural Engineering opens a menue at the start with all information on megastructures, and you can ajust traits, disable and re-enable features, ect ect.

maybe you could do something similar. At the start, a menue opens up with a slider (Or a box you can type of), that has a default of forty. But, you can ajust it. If a slider, anywhere from 0 years to, say 999. If a text box, any number.

Just an idea for how to make the truce timer configurable.

Two major problems:

The diplo modifiers kinda ruin the diplomacy. They swing between -300 to 300 and back within a few months.

Every AI tries to be a Crisis Aspirant. LOL. Even the peaceful traders. And every AI does the exact same thing: rush to cruisers and mass them. Is there some way to keep the econ changes but make the AIs more flavorable?

Is there a way to keep the econ changes and initial 40 years of peace, but give the AI more leeway for developing their empire so they don't all do the same thing?

EDIT: Nvm. I saw the Starnet friendship patch mod. Thx. I'll try that.

Is there any particular reasoning for a lot of the changes you've made to the "common\resolutions\01_resolutions_nemesis.txt" file? It almost looks like Paradox devs changed the file in an update and you haven't updated the mod in response. If so I would be grateful if you updated it.

Your file removes a lot of conditions that seem detrimental to do so. In particular, and the reason I bring it up, is because your file does not make use of the "declare_crisis_war_effect" scripted effect which is becoming a compatibility problem for me and one of my mods.

Feature request:

Since this mod does tend to make AI focus on science. If you could code an event that triggers when a federation member votes down an AI request for war, then not have that AI ask again for a long long time on the same empire.
Seems like the moment I decline a war in my fed, the AI will aska gain in several years and will continue to do so until its upset and leaves the fed.

I have no tight control over how frequently the AIs request a war.

There's a problem with worker job weights. Miner and Farmer have big weight modifiers for non-droid robots, but other worker jobs don't. Since robots can work basically all worker jobs now, Technician and rare resource worker jobs should have the same weights, otherwise robots will never take those jobs even if their traits are better for them, unless all the Miners and Farmers are robots. Currently I'm testing giving those 6 jobs this:

This fixed my immediate problem, but I'll see if it helps or hurts once I have droids and/or indentured slaves.

Something that I've noticed is that, either intentionally or due to a bug, whenever there's a machine empire in one of my campaigns, unless it's a determined exterminator, they'll start aggressively expanding outwards, declaring war on anything and everything that gets in their way, to the point where they'll conquer the entire galaxy.

The worst part of this is that other empires don't seem to see this as a problem, as since they aren't determined exterminators it's nigh impossible to have them declared a crisis since they assign all of their envoys to the galactic community, which usually guarantees them a position on the galactic council, and enough diplomatic weight to prevent a crisis declaration on them from ever being voted on, even without veto power.

Please, PLEASE change this, it feels impossible to get anywhere without getting my teeth kicked in by a machine empire, even on ensign.

Thanks for the feedback, I think the best way would be to increase threat generation so AIs are more likely to ally against the machine empire, correct? @Hibimiku-9000

I think that should work. Either that, or just make Machine empires either worse at, or slower with setting up their economy.

Great mod I've ran I've been running ai games to see how they do and I've noticed the ai never seems to pick the expansion tradition tree, seemingly ever they sit around with an empty ascension perk slot for the entire game, seems to be every ai no matter what. I am running the conquest and population balance mod but I don't think that would effect it? Other than that the ai cant seem to scale up its shipyard production I had a 20 million fleet strength ai making 14k alloys profit a month sitting on only 6 starbases with shipyards and no megaship yard, it couldnt outscale the maximum difficulty crisis just because it refused to build any shipyards and wouldn't replace the ones it lost even though it had over 80 upgraded starbases, thats probably much tougher to fix though.