The mana pool is a good idea, all these concepts sound like the Age of Wonders system: with "shards" instead than "nodes" but that definitely works so I have no problem with it.
Still you have a few overpowered units in the game. The "spy" for example can be devastating: it can inflict 20 points of damage per turn on turn one to every single enemy units. Make an army of them and nobody will be able to survive turn 1 of any attack.
Regarding the AI, I followed the way AOW evolved, they tried different things and in the end I believe the best tactics for sovreigns is to stay inside their capital, not just next to it: but INSIDE. In this game if the sovreign is close to his city the city can be taken making that instantly an enemy territory (by saving and reloading the turn at the moment). The sovreign can then immediately be attacked and killed, game over for them. Also I am perplexed that the sovreign cities disappear once he is gone.
I believe all those armies and cities should become hostile and aggressive against the player. Call them "neutral" cities or "rebels" but they can just keep the flags and insignias of their former affiliation even though their faction is dead. You don't even have to change their look in fact. (Notice that in Age of Wonders Shadow Magic that's the way it works, only in that system the sovreign once killed respawns only inside his tower assuming he has one. With this system in EWOM the enemy ruler would be much harder to kill making this game more challenging than AOWSM since a sovreign who stays in his city becomes virtually impossible to kill until he has cities to respawn to... But maybe not all sovreigns should be pursuing such strategy...) - Also the AI should become extremely aggressive with players who are pursuing an expansionistic strategy (after they have killed several sovreigns).
In most games of this sort when you conquer an enemy city you better keep an army in it or the population will revolt. In some games even creating armies out of the blue (Total War) - That slows down the advance in enemy territory in a realistic way since some troops have to be left behind.
The tech trees should be IMO related each to a specific resource: Imperium=Food - Sorcery=mana - Domination=Gold, so that each of them would have to be researched (it's already a bit like that but it could be enhanced)
Regarding the combat system take a look at Heroes of M&M, there are great ideas there, and I would suggest to make bows and certain spells more or less powerful according to the DISTANCE from the target. Also I would speed up the animations, but that is obvious.
Mana regeneration is more important than the total essence. The tower of magic should speed up mana regeneration, not give lots of essence which I will never be able to reload anyway.
Do we really need diplomatic capital points? I always use them to buy whatever I want from the enemy before killing them off. If I am pursuing a non diplomatic strategy they are just a big exploit
....An please most of all GET RID OF ALL TELEPORTING SPELLS!!!! They spoil the game making the beautiful geography of the map completely useless and making all games be the same with just a super stack jumping around (teleport is a SCI FI device not a fantasy one!!!)
Hopefully we'll be able to get a Play By E Mail system some times, since I doubt multyplayer LAN will be very popular in a game that takes so long to complete. After all PBEM is what keeps Age Of Wonders alive after all these years.