ASW – Alternative hero leveling.

In addition, each ability should belong to only one skill and not depend on others (except: ultimate abilities as descendants and racial abilities as ancestors).

So, you'll remove all dependencies between the "schools"? Will you only leave connections with racial skills? This will definitely simplify the skill tree (this is not a criticism).

Added 2 minutes ago
My suggestion for Fire Arrows: move them to the Machinery skill after Sulfur Rain. This way, the player will either upgrade the rapid-fire ballista or siege weapons through the catapult. Having a choice is better than having none (siege weapons + rapid-fire = an overpowered ballista, but individually they are weak). It would probably be a good idea to strengthen the basic ballista.

Added 2 minutes ago
Hmm, I looked it over - your siege weapons are an alternative to rapid-fire. But this is a very weak alternative, in my opinion. Since the double shot with siege weapons is significantly better than the triple shot without them (+ an extra perk for the catapult).

Added 7 minutes ago
I think the best solution is this: swap the perks of rapid-fire and the ballista (as well as the catapult and Sulfur Rain).
That is, the basic ballista gives +1 shot (damage x2), the advanced one gives another +1 shot (damage x1.5) + control + durability x2. The same for the catapult.
Tie Fire Arrows as an alternative to the advanced ballista (between the basic catapult and ballista). This way, there will be a choice: double shot with siege weapons, or triple controlled shot (and doubled ballista durability).
In addition, this will increase the incentive to upgrade the advanced Machinery skill (advanced perks are better than basic ones).

I'll clarify right away: in WGE, siege weapons are planned to be placed as a level 3 catapult, i.e., incompatible with either the controlled or multi-shot ballista. But there, siege weapons are much more powerful.

Added 11 minutes ago
Another idea: to simplify the skill tree, move all unique perks (Wide Gates of Hell, Rune Recall, etc.) to the racial skill, while preserving the corresponding incoming connections from the "schools". In addition, standardize the upgrade of each "school" for all factions (except the Barbarian). That is, move all the differences to the racial skill.

This will provide: simplification of the skill tree + alternatives for what to upgrade in the racial skill (currently there are few: there are 3 perks for every 3 levels of the racial skill).