I read through the whole thing and in regards to the Skill Tree, I think you are going in the wrong direction.
What I think is not a good idea is that you mix Passive Skills and Active Skills together - at least if my understanding is correct that you unlock Passive Skill Points by spending Active Skill Points into Nodes that unlock (additional?) Passive Skill Points - , instead of separating them into two distinctively different Systems and let each System have its own Points (Skill Points for Active Skills and Talent Points for Talents/Passive Skills).
Mixing the Active Skill System and the Passive Skill System together will cause them to compete for Skill Points, which imo is not a good thing in this specific case.
It is good that players can not get everything and have to make meaningful choices, but just like letting Charm compete with Inventory Space in Diablo 2, letting Passive and Active Skills compete for the same Points is detrimental.
Say what you want about Diablo 3, but one of the things that it actually did better than D2 was that Passive and Active Skills were separated and during D3’s development, you could spend Points into both Passive and Active Skill separately (Trait Points for Passive Skills and Skill Points for Active Skills), as you can see here:
However, this all is based on my assumption that you gain (additional) Passive Skill Points by spending Active Skill Points into Nodes on the Active Skill Tree.
I might be wrong with that and may have misunderstood something, dunno, but if not, I think it is better to tell you now so you can eventually revert this issue if you desire to.
There is another issue with Skill Systems that take the form of a Tree (regardless of them being for Active or Passive Skills) is that you have to waste Points into pre-required Skills, Talents or Nodes, just to get to the Skills, Talents or Nodes that you actually want.
A solution to this is simple: make it a Skill List and a Talent List instead of a Tree.
There still can be Skill Trees for each individual Skill, like in Last Epoch, where each Skill also has its own Skill Points (that can be spend on basic upgrades, but also on effects that completely change the way a skill works, like Runes in Diablo 3).
In the Passive Skill System some Talents can be connected to prerequired Talents if it makes sense for these two Talents to be connected.
You even can have Normal Talents (with Ranks that you can progressively upgrade by spending one point after the other which give more basic bonuses) and Major Talents (that significantly change how a Skill or Mechanic works, similar to PoE’s Keystone Passives), which costs several Points at once to unlock, without needing the system to be a tree with pre-required Passive Skills.
A few Examples:
forgive me for using D3 images, but it was the best that I had available at the time of me making this post to illustrate what I was describing
What I am suggesting here is not a demand that you put it in the game, it is just a suggestion for an alternative which solve the intrinsic problems described above that lie in the very nature of Active and Passive Skill Systems that take the form of a tree.
But if you don’t want to go in this direction, then I understand and respect that (since it is your game and your vision), although I disagree with that particular design decision.
Lastly one good thing that I wanna point out is your decision that players will not be able to unlock every Active and Passive Skill. This is good since it creates very different and distinct builds as you pointed out in the blog, but also because it forces players to make meaningful choices.
Unlocking 30% of what is available sounds like a good number (though I personally would like to have 7 Active Skill on the Hotbar instead of just 6).
The Enchantment System sounds interesting, but before I can give it more and better feedback, I have to think a bit more about it.
But that you for the blog!
It was a good read and I think it is good that you share some of D4’s development process with us.