I will say if you have your own mod and like any of these changes please do use them. They're mostly just fixes or logical changes and not me expressing my own creativity so I'm not possessive. Use as you like.

Many mercenaries had bad combat roles and weren't updated with Crusade. I've fixed them so they should all be of use.

Redid all the threat/fortitude/value settings for ship equipment so improve the auto designed ships roles. I found it works pretty well. I factored in range, fire rate, and accuracy, but the end formula is as follows:
beam threat = 0.65 x square root of power
missile threat = 0.74 x square root of power
kinetic threat = 1 x square root of power

shield fortitude = 0.2 x strength
point defense fortitude = 0.23 x strength
armor fortitude = 0.13 x strength

Value is reduced for engines and life support to prevent combat ships from being made support class. Weapon augments give about 2 to change medium assault to capital class. Also reduced value of medium hull so the assault/capital change over will happen when appropriate.

Guardians now follow escorts first and supports second. This allows guardians to contribute to the fight instead of waiting until the battle's already lost before fighting. Interceptors still must target guardians first so supports aren't made more vulnerable.

In addition to hitpoints, ship levels increase evasion. Ranging from +4% per level for tiny hull to +0 for huge.

Changed one carrier designtemplate to a cargo hull because one can get them far earlier than large hulls but not use them unless a design existed.
most equipment said it had maintenance but the game didn't charge it. Those were removed for clarity but added maintenance for really good equipment i.e. tactical repair, fleet wide bonuses, and fighters. 1 credit per fighter including on starbases and orbital defense improvements.

Here's the general philosophy for the ship template changes I made:
Every size/weapon still has a no resource design.
All large and huge ships and medium escorts have tactical repair.
Huge ships are hybrid attack/support as they can fit so much firepower that even alone the fleet attack bonus is better mass use than more weapons.
Designs use thrusters based on their weapon range and tactical speed. i.e. large kinetic often, small missile rarely. Also escorts for evasion and to keep from getting left behind.
The AI can't be trusted to use escorts to defend "glass cannon" ships the way the player would, so most ships designs have defense, but often only after enough weapons to prevent them being classed as escorts. Difficult to do with varying technology so I can't guarantee the results are always right.
Kinetic ships however prioritize defense for the best effect of their short range, low damage, rapid fire weapons which benefit from drawn out combat so are often escorts.
Medium ships are escorts, regardless of weapon, except for those with weapon augments.
Carrier's also carry point defense and shield projectors.
Transports use speed/range support modules to make escorting them easier.

Starbase modules now all give small hitpoint increases, and the military ring gives +50%. Some resource costs reduced when it could take 100+ turns just to break even. And the resource specific modules now give x2 of that resource rather than 0.1 which would just about never pay itself off.
The defense increases from modules increased relative to the effectiveness of the weapon they defend against.

Carrier modules now cost 1 upkeep per fighter they give to balance them essentially being free, expendable ships not needing resources. Now, fighters are for the money-rich, capital ships for the resource-rich.

Lots of colony improvement tweeks
Fixed influence values that were insignificant
Colony improvement that add to base output now also increase maintenance. The human player can do adjacency bonuses much better than the AI so this evens out the advantage a little, and gives a use for maintenance reduction effects (mobster citizen). It's 1 per 1 raw production, basically cancelling the money gain while keeping the social, ship, and science, and  0.25 for them individually. But not wealth because that would be directly negating itself.
All tourism improvements weakened, and don't give adjacency levels to each other, but the levels bonus is better. Also almost all tourism bonuses that only increased existing tourism changed to give base tourism which should reduce confusion. Trade routes have been made more profitable. Tourism was almost free money since a small investment generated increasing income forever, while trade routes were more work to establish and could be cut off easily by war so this evens them out a little. Tourism will still be very high in large galaxies.

Events adjusted to give correct effects when they mismatched their description. Also some culture choice which were definitively worse for one alignment over another got extra culture points. Only if they were the same but better effect (+10% economy vs. +15% economy) not if they were different (+10% economy vs. +10% approval).

Divided the improvements unique to synthetic between it and cybernetic ability which previously just had mechanic citizens despite the description implying otherwise. So a civ like the Yor have both they're unchanged. If they're just synthetic it's still a constructed population like Blade Runner replicants, but not interconnected with outside equipment like Star Trek Borg.
Scavengers get back the stolen technology they previously shared with the Iconians, Altarans, and Drengin. Snathi changed from slavers back to unrelenting now that they have slave mills anyway.
Some combat related effects from Traders moved to War Profiteers.

Some culture traits improved, especially the culture points given by one per civ improvements. Also the AI flavor settings changed so the AI will pick ideological perks based on their personality.

Theocracy government now from devout ability, and Unity now from certain ability.
Non-combat government ships lose life support to attempt to keep them from leaving home, and also given AI tags similar to some mercenary ships with similar purposes.

Fixed the extreme planet tech requirements. The classes of bonuses (or penalties) were set so the earliest tech gave the best bonus and the later tech did nothing. It's sorted out so it increases with tech, maxing out with the unique ultimate adaptability tech which previously did almost nothing but promised a lot.

Black markets now available with numerous abilities instead of just one specific pair of abilities if used together.