I didn't have much time last night to play around with it, but I agree with the spell issues. Some quick thoughts:
The spell info 'page' does not display Essence cost - spell card (from character spell tab) shows both Mana & Essence costs. I want to know how much Essence the spell costs to cast, before I learn it.
I think there should be 3 'types' of spells. Generic (anyone can learn), School specific (must have the school, can be chosen at creation or maybe found as a book/reward), and Shard based.
Hmm... If I create a Sovereign with no schools of magic chosen, I would be able to learn Generic spells, through research. If I want to learn Shard spells, I need a city tapping a Shard resource. But I would not be able to learn School based spells at all.
Let us learn schools, possibly from a quest reward, or random cache reward - but those should be 'phat lewt', rare & with tough guardians.
On the other hand, if I create a Sovereign knowing the Fire School, I should be able to learn 'minor' Fire magics - Firebolt & such. If I want to get the Wall of Fire spell, I need to build a city at a Fire Shard, and research it.
'Epic' spells should require both knowledge of a school and access to a Shard of the same kind. Maybe anyone learning the Fire school could throw a Fireball, and anyone controlling a Fire Shard can raise a Wall of Fire - but you need both the School & Shard to raise a Volcano.
I would rather have a similar mechanic that Master of Magic used, instead of how it is currently. (Not sure if you can change it at this point) Instead of being able to learn anything that I had spell points for, with points growing to a limit, I would rather set a 'Spell Research target', and have the points feed into it until completed.
Either that, or you need an extra icon on the left icon bar, that lights up when you are at max spell points again.
Perhaps the Loremasters would let you set multiple spells to learn, instead of simply giving spell points.
Love this type of spellbook organizational idea!
Recommendations: Having the spells arranged in a Book:Function matrix would be both quick and expandable. So across the top you would have something like Favorite, Fire, Air, Water, Earth, Summoning, Ruin. Upon selecting any of those top tabs, the side tabs would appear and have categorical fields based on the primary selector. I.E. Selecting Air, would bring up sidetabs like Direct, Area, Combat persistent, Combat buff, Enchantment, World and such. Favorite Tab would allow you to make a custom quick list for rapid spanking action.
Also love the idea of a slow Essence regen. I read that you are changing city creation to requiring the Pioneer Pack, and the Sovereign starts with only one. So, all the Sovereign can do is found one city then run around and create a lot of fertile lands - but you still have to train the Pioneers to start new cities. With the changing of the city founding mechanic, you should rethink the permanent loss of essence.