Frogboy was asking for some specific suggestions regarding the magic system in another thread, so here goes.
Sovereign creation:
Right now while creating my sovereign, I get no clear indication on the spell books. There is no information on their purpose, or how significant / insignificant it is to choose a spell book. Spell books should probably be given their own separate page on the sovereign creation screen to outline just exactly their purpose is. Similarly to MoM, players should be able to dictate the number of spell book volumes they wish to have from the start (see the spell book volume section below for more info).
Importance of unique spell book spells:
Spell books should be significant, game-altering objects. Choosing the fire spell book rather than the earth spell book needs to directly change how the game ends up being played. Each spell book needs to provided possible access to original and unique spells to that book - spells that provide the same function but operate under different names shouldn't start appearing in all spell books. An example of what shouldn't end up happening: Earthquake (earth spell, slows down enemies), Gusting Winds (air spell, slows down enemies), Icy Ground (water spell, slows down enemies), Heat Haze (fire spell, slows down enemies).
Spell book GUI:
As I said above, spell books need to provide original spells - not spells cloned from other books to be then used new names. So if the spell books are to be each so unique, there needs to be a clear way of access the spells from each spell book - and seeing what spell books you have access to. The magic page then logically needs a massive GUI revamp: Either split the existing spell book into sections (similarly to MoM / HoMM) or better yet display a bookshelf containing the spell books you've found so far. Clicking on the binding of a book would expand it to show the player what spells they current have access to. It might be a wise idea to have the first page include some sort of introduction explaining the "mind set" of the book (used mainly for evil purposes? dispelling / protecting against magic? etc). In the interest of convenience, it would be nice to save the last page being viewed - so that when the player goes to re-open the book, he / she is brought to the same page.
Finding spell books & spell book volumes:
So if spell books are to be so unique, game changing and important, then clearly they need be acquired in a far more exciting and dangerous way than just being "researched". Therefor spell books should be in no-way acquirable through research. Spell books need to become physical items that can only be found through conquering enemy civilizations, killing enemy sovereigns (loot) or finding them through goodie huts / quests.
In order to prevent all civilizations from having the exact same magic, spell books need to be split into volumes. To avoid overwhelming the player, this system would be extremely simple (but effective). Using the bookshelf concept from earlier, each spell book would simply expand in width upon finding another related volume rather than actually adding another book to the shelf. On an important note, volumes would not be numbered, (ie, the player would not find volumes I, II, V) but instead would simply be greeted with the message "You've found another spell book volume for _____ further increasing your potential knowledge of ____ magic".
So how would spell volumes somehow prevent all civilizations from getting access to all of the same magic you ask? Quite easily since spell book volumes will be limited. As said before, sovereigns need to be customizable with the desired number of starting volumes of a specific spell book. Sovereigns shouldn't be able to start will all volumes ideally (for example if the fire spell book consists of 6 volumes, the sovereign should be limited to at most 3 during customization). Upon starting a new game and creating the world, X number of spell book volumes will be placed throughout the world for each spell book where X will be calculated (based on the # of starting sovereigns) to provide only 25% - 50% of the starting sovereigns access to an entire spell book's set of volumes. Of course that doesn't mean that 25% - 50% of the sovereigns will be able to complete their sets due to the fact that other sovereigns will be wandering the world as well.
Bonus points: let player customize the number of spell books / spell book volumes available when creating a new world.
Double bonus points: create spell books consisting of just 1 volume that contain extremely advanced / destructive magics. Imagine being the only owner of the "Daemon Mastery" book.
Spell / spell book research:
As mentioned above, spell books need to be found, not researched. But once you've found a spell book, how do you get access to it's hidden knowledge? Instead of spending spell points on researching specific spells, players will be able to focus their spell points on researching one of their current spell books. The research system will function like the technology system: upon reaching the required number of spell points to learn a new spell from a spell book, the player will be presented with the option of selecting one spell from a small selection of spells from that specific book (based on spell difficulty). Obviously the more spell book volumes that the player has collected, the more they'll be able to research from the book in the long run (with each volume adding more powerful / rare spells that can be researched).
Spell books / volumes as a resource:
Since the world will be filled with a limited number of spell book volumes, wouldn't it be nice to be able to do something with unwanted / excess books? Players should be able to use spell book volumes as diplomatic resources (selling, trading, w/e) with other civilizations.
It doesn't make a 100% amount of sense, but since we're already informed on other civilization populations / powers it would be fun to be able to see the number of available spell volumes in the world as well as well as being able to see specifically what spell book volumes other civilizations have access to. If one civilization has an entire library worth of books, the other civilizations in the world may feel a need to form a temporary alliance to deal with the situation. 
Overview:
Since there is a lot of text above, I've reduced the core concepts to a small list to re-iterate through the primary ideas:
- Spell books need to be important and contain access to unique spell trees. No spell clones!
- Spell books need to composed of a set number of volumes. The more volumes a player has, the more spells they can learn from that specific field of magic.
- Spell books need to be a limited resource to prevent civilizations from all ending up with the same magic by the end of the game.
- Spell book volumes need to be found through quests / conquest rather than research.
- Spells should be learned by spending points focusing on specific spell books and then selecting 1 spell from a small set of randomly selected spells from the appropriate book.
- Spell book volumes need to be usable as a diplomatic resource.
- Let players see what spell books are available in the world, and see what other civilizations have found.
- Make a separate page for sovereign creation that focus on spell books to ensure the the player fully understands how important they are.
- Allow sovereigns to be customized with varying numbers of starting spell book volumes.
The above bullet points is just a quick run down to add some clarity, I'd urge any developer reading this to go through the actual text.
Hopefully my ideas and concepts outlined in this post will be of some help.