UI
Something in my game setup was causing the situation button to vanish after opening the magic perk trees window. Not sure if this is your mod's solo issue or if that's a conflict. It's not a huge issue either way as it reappears after opening some other windows.

Perk prerequisites are not properly documented.
Spell descriptions lack the info about the costs.
Building descriptions lack info about magic-related effects. Put them into the flavor text if you have to, but don't leave things as is.
Mana circles also lack information about T3 construction prerequisites.
IIRC your tutorial doesn't explain those buildings either.

Content
I'm getting a weird impression about this mod's development.
I'm comparing this mod to how it was back in around the times of 1.3 and I can't help but wonder what the heck were you guys doing all this time. I mean... I can see what you've been doing but what were you thinking when you were doing that?

Maybe that's just me but... a new government type? I don't think that's what a magic mod should be about. Do you?

And your custom UI for the magic perks. What was the point? Your sets of perk trees are still pretty much what you'd expect from vanilla focuses, give or take a few minor quirks. PoD (Princes of Darkness) used vanilla focus UI for it's disciplines just fine. Other than looking slightly more fancy I don't really see what you've achieved with this.

Meanwhile the core of the mod – the spells themselves and the magic system are practically the same as they were. No new trees, almost no new spells, and almost all the same old balance issues.

Being able to see the mana on the hud is definitely a needed improvement though.

Balance.

Overall the beginning feels underwhelming, but before you know it that's gone and you're OP AF.

Time tree feels like it's the closest one to being balanced. It still isn't though.

Healing tree needs trimming down. The passives you get are too strong, the spells however are lacking. Mostly in variety. But also they are inherently boring. But then again, it's a healing tree, so what can you expect, right? Cut one longevity perk and one casualty reducing perk. Cut those values on the remaining perks by half as well. Add some new recovery types spells. Stress recovery seems like a good choice.

Mind tree is OP but there isn't much that can be done about it without changing the core magic systems. Raise the costs for now as a slight stopgap?

Genetics singlehandedly cancels out the worth of an entire focus line. Honestly I dunno if it's OP or if it's not. It definitely takes a whole mechanic out of the core game though.

Necromancy is also OP. That 600 mana kill alone can move mountains if you know how and when to use it. Basically same issues as with mind tree. You can also drain an old ruler with life drain to a much quicker death for NO negative consequences for you whatsoever. Army spawning is also OP.

Elemental doesn't have anything we haven't seen already - OP summons and auras that go from weak to OP AF as your mage level goes up.

It's hard to say much on the subject when I don't know where you want your mod to be balance-wise. It's definitely OP but that isn't the real issue here. The real problem is that it's OP in ways that kill a lot of fun in the game.

Take immortality for example. Inheritance mechanics, post-succession issues, genetics, learning speed. It detracts a LOT from the main game.

Playing your mod without immortality is actually kinda underwhelming though... because near the start of PC's career magic is actually weaker than vanilla focuses.

Once you live for a while and get the buildings though it really picks up, and by the end of it it feels like nothing will EVER be out of your reach again. It may be a fun goal to go towards but once you're there it's not a fun place to be at and you get there in under ~2 generations worth of time.

This is WHY I think that working on core systems (such as more complex spell casing) is crucial and should have been your first priority.
The draw of magic is always about getting the things you normally can't. But if you can just get them without having to do much in the process, well... it's BO-O-ORING.

But while that isn't there I'd snap at the power levels if I was in your shoes.

Cut the cost on most auras from 15 to 10. Cut the per-level effects of most auras to ¼ or 1/5 of what they are now, but raise the starting values from zero to something. For example the tax increase should be fine at around 10% + 1% per 2 levels.

Immortality for 30 mana per month is too cheap though. Try a 100, and no soul forging.

Summons should stick to a fixed troop per cast and per mana rate. Instead use mage level to limit the total amount of them that you can have.

Make undead much stronger but proportionately less numerous, AFAIK vanilla's dynasty head selection mechanic doesn't care if your troops are elite or garbage - it only cares who's got more heads under them. Also don't forget - vanilla warfare is mostly about morale – ATT and DEF mostly reflect how good a troop is at routing the enemy and not folding under pressure. You'd think the walking dead of even the weakest kind would excel at that as they are both fearless and inherently frightening. Yet in your mod they are worse at it than a pack of untrained peasants AKA levies.

For most of the negative effects you can inflict on someone there should be a negative opinion to match. I life drain an old dynasty member who's title I'm elected to inherit, and no one gives a damn, neither he nor his vassals, nor my vassals. Vanilla would have me win over his court, arrange an assassination, and live with a fear of being exposed as a dynastic kin-slayer. And that's just one example of many. See what you're carelessly trampling over here?

Likewise there should probably be a positive modifier for the good things you do for people. Healing or improving genetics should probably come with an opinion boost and maybe a chance to form friendship. You'd think my associates would care about me curing their cancer or fixing the frailty that their mom's incestuous adultery has bestowed upon them from birth.

Education

I frankly don't see what's the point in having a magic education in-game. It creates more issues than it's worth in terms of fun. Focus selection UI issues for one. Gimped AI's that can't use magic well for another. And then there's a question of how it looks simulation-wise. It probably makes sense in that magocracy of yours, where magic is legal, but in the rest of the world...
-So what have you been teaching that ward of yours?
-Oh, nothing much yet, just some basic magic principles for now.
-BURN THE WARLOCK!
Vanilla, as you may have noticed, puts esoteric practitioners (witches and wisemen) under learning and for a good reason - they FIT there. It provides both the necessary educational background and the necessary plausible cover.
It's never explicitly stated WHAT you're learning you know, so it fits both the mages in magocracy and the mages in hiding. When most of the world is illiterate (nobility included, although PI seems to have missed that part with all those book artifacts) only the other scribes would know one book from another.

Ley lines.
Unless I missed something to build a mana circle you need a duchy capital on a ley line.
That feels weird. For example there's this duchy on the border of Scotland and Ireland...
11 total baronies in 4 counties. A ley line passes through 8 out of 11 baronies, and 4 out of 4 counties.
The 3 baronies missing the ley line are a very small part of it, but capital barony of the capital county of the duchy is one of them. It's one of the most “ley'ed” duchies out there, it basically stretches along the ley line. But you can't build mana circles there cus the capital “side-stepped” it.

Then there's a balance issues with them. Mana circles are OP, much stronger than any normal duchy building IMHO, yet you don't even need to own the duchy to build them.

I'd re-do the ley line map if I were you. Calculate how many counties in duchies are on the ley line and give the duchies' capital county a modifier based on that number. Then make the circles require the entire duchy like the vanilla duchy buildings do, and for the sake of balance make them give a progressive levy and tax and development MALUS for the entire duchy. There's a common belief that the ley lines makes habitats “better” in various ways, so that fits both the balance (like I said, they are OP) and the lore. Whatever it is that you're extracting, you're robbing the land of it.

And those were my opinion and impressions of your mod. Do with 'em what you will, and good luck with whichever direction you decide to take your mod.