I made the starting hero your "Commander".  Significantly stronger and more gameplay defining than random heroes you'll recruit further turns into the game.

Note: All existing heroes unchanged.

Hero Overview:

Enhanced Skill Tree:

WIP:  New ship, medium class.

In balance testing: 91 new skills!!

The new skill tree helps shape your starting choices.

Seeker (Blue):

Tier I

Science per pop +1 to +3

Influence per pop +1 to +3

Tier II

Science per hero level +1 to +3

Technology Cost Reduction per Trading Company -0.5% to -2.5% (Senator skill, not effect if not on Government)

Diplomacy Cost Reduction per Trading Company -0.5% to -2.5% (Senator skill, not effect if not on Government)

Influence per hero level +1 to +3

Tier III

Trading Company EXP 40% to 200%

Tier IV

Hero Assignment Cooldown -30% to -90% 

Guardian (Red):

Tier I

Fleet Health 20% to 60%

Fleet Movement 1.5x to 3.0x and Vision 2 - 4

Tier II

Fleet Damage 40% to 200%

Fleet Shield Absorption 20% to 60%

Tier III

Fleet Health and Hull Absorption 20% to 60%

Fleet Manpower Refill 40% to 120%

Fleet MaxShields 30% to 150%

Tier IV

Fleet Hull and Shield Piercing 10% to 50%

Overseer (Green):

Tier I

Industry and Food per Pop +1 to +3

Dust per Pop +1 to +3

Tier II

Industry and Food per Hero Level +1 to +3

Building Cost Reduction 10% to 50% (On System hero is stationed at)

Dust per Hero Level +1 to +3

Tier III

Strategic resource +1 to +3

Luxury resource +1 to +3

Tier IV

Industry Food Dust +10% to 50% (On system) +5% to +25% (On Empire if Senator)

Approval forced to Content - Happy - Estatic (On System hero is stationed at)

Here are some larger pictures:

Overview

https://postimg.org/image/mscztkywj/

Skill Tree

https://postimg.org/image/r2g7vsri5/

It might be hard to see but skills either have 3 to 5 levels each totaling 30-31 points per specialization.

While a normal hero might spend one point in Generic for 80% dmg, then two points between Faction and Specialization for another 40-80% the commander spends five points in a single skill for 40% - 200%.  Allowing for similar growth at similar points but coming out ahead if you choose to focus.

There is one glaring flaw with the system I'd like to figure out how to change.  Right now you can go deep into one specialization then tag the top tier traits in the others.  I feel this works and doesn't work for gameplay.  At a later stage in the game you need stronger traits per hero level.  Also I've made efforts to make the higher traits rely on lower traits for full potential.  However, if I had my way I'd like to limit unlocks to five points in each specialization per tier unlock in that specific specialization.

Also I have no idea what purpose masteries serve.  Future content?