Here is my idea for "Governance" rework. Instead of the agenda and council bonus you'd get from the vanilla Statecraft, it revolves around making the empire more efficient, essentially becoming more of an empire boost than a leader boost.

>Edict fund, Central Administration and finisher stay. These are very good in and of themselves and form the basis of the tree.
>Controlled state should change for something else as ethics attraction can be useful, but can also ruin plans for reforming out of an ethic later (Factions disappearing). My thought here was to have a "Focus" policy unlock: This policy gives a minor boost (3-5%) of a given area of the empire. Examples: +x% monthly research, +x% monthly alloys, +x%trade value, +x% strategic resources, etc. It shouldn't be as strong as Prosperity, but basically a tag-on to help an empire grow.
>Service Arrangement should be changed to +happiness instead of Amenities as with even base-game bonuses you can get plenty of amenities on larger worlds. Happiness would allow for more pop happiness, which reduces crime and increases stability passively.

Now, for the Leadership rework: This tree would focus more on bringing up new leaders and allowing you to have a genuinely leader-focused empire with more capacity.
>Galactic University stays, maybe even giving a +1 leader cap now...
>Knowledge download should go to 2.5/3 exp a month if affected by exp gain bonuses to not overshadow Offspring hives. Pairing it with a +50% leader upkeep would work very well.
>Internships is swapped to start leaders off 1 level higher. This allows recruiting better leaders early.
>Extended Schooling is changed since all leaders go to 10 anyways. Instead, it is now changed to adding a +2 leader cap, allowing more leaders to be recruited.
>Finisher could be kept as a special trait, or a trigger edict for resources to give the trait to one of your leaders, improving his abilities and boosting him/her up a level. Would also be great to get a ruler version with e.g. -empire size penalty.

Perhaps we could have two leader-centric tradition trees: one that focuses on empowering individual leaders, and another that rewards a wider pool of leaders. I've seen many a complaint about the restrictions on the new leader cap mechanic.

This all said, I haven't played the game since 3.8 dropped, so I've not seen what the new official trees do yet.

Paragon's Statecraft: Focus on Council and stuffs

Mod's Statecraft: Maybe focus on bureaucracy and streamlining of administration? Can be rename to something like "Bureaucracy" or "Administration". And provide some bonus for Governor leaders.

As for Mod's Leadership, maybe make them more focused. Compared to Paragon's Aptitude, Leadership tradition focus on Army and Navy leaders specifically. Maybe rename it to something like "Commissariat" or just simply "Command"

Paragon's Aptitude tradition will just be a general buff for leaders. While the other two traditions buff specific types of leaders as mention above.

Alright agenda ideas
first Initial effect then Launch effect

Industry:
Expand Fabrication: Workers 5% upkeep redution / Workers 20% upkeep redution

Science:
Affordable Experimentation: Researchers job 5% upkeep reduction / Researchers job 20% upkeep reduction and Researchers produce +1 to each research

Navy:
Modernize Armada: Ship upgrade cost 10% less and upgrades 20% faster / Ship upgrade cost 45% less and upgrades 50% faster

Government:
Enforce the Principles: +10% Faction unity production / +20% Faction unity production

Leadership:
Bolster the Guidance: Reduced leaders upkeep 10% / Reduced leaders upkeep 40%