This was the Mod I was working on one year ago or so but I never finished it. I recently started to think about it again because we still have no (working) mod for ERA which expands the skill system as far as I know.
Now seeing your ideas I thought they are very similar, so I can share what I did.


Advanced Classes Mod
The aim is that we get some kind of class distinction between Adventurer, Warrior, Mage heroes and extended options for big maps and high levels. It should increase replay value and every class should feel strong and fun to play.
Looking at the secondary skills in heroes you roughly have 8 might skills, 8 mage skills and 8 adventurer skills.


*Mage: The mage boost the stats of his creatures with strong defense spells. By studying all elements he has access to powerful combat spells which he can cast several times to destroy his enemies. Fight the mage as soon as you can or his magic will become unstoppable.

Air Magic
Earth Magic
Fire Magic
Intelligence
Mysticism
Scholar
Sorcery
Water Magic


*Warrior: Good understanding of combat tactics and strategies the warrior itself increases the damage of his troops with his great combat knowledge. He also boasts the morale and luck of his troops. On the highest ranks, his troops will do insane damage with attacks.

Archery
Armorer
Ballistics
Leadership
Luck
Offense
Tactics
First Aid


*Adventurer: The adventurer is a swift explorer and no one is faster than him. He strengthens the hit points of his troops in combat and with his knowledge of first aid and spiritual magic he will resurrect his fallen troops after every fight. He is also excellent in managing his kingdom. On grandmaster level, his army will outnumber any other army in Enrathia.

Eagle Eye
Estates
Learning
Logistics
Pathfinding
Resistance
Scouting
Artillery

Neutral Skills
Wisdom
Navigation
Necromancy
Diplomacy


Now my idea was that you get class points for each skill you pick. (see the picture below)
By reaching a certain amount of points you advance in that class. Each class can have 3 or 4 levels. Adept, Expert, Master and Grandmaster. It is only possible to reach Grandmaster rank in one class.
By reaching a level you can choose additional perks for that class. Lets say you pick all Warrior skills you will become a Grandmaster Warrior. After you have maxed out all skills your hero class is determined. For every level, after that, you will be able to upgrade one of your secondary skills to Master/Grandmaster which can only be acquired by that class.

I already put some thoughts in this concept and have done some serious scripting on it. But I drop this idea some time ago. So maybe if someone says he wants to team up with me and finish it, why not. The outcome can be different and I am open to new ideas.

This is how I imagined the point distribution for every skill.


I also wrote a Bonus/Perk table for every class but these were just details.

You see, the concept is similar to yours but not so distinguished with good and evil and subclasses. Always start small, it can be expanded later on. Best ideas come during scripting anyway