I'm not talking about organization and interface, the system itself is a mess.

List of current complains I'm aware of. (for convenience)

• Essence system is "malfunctioning".
• Wisdom is not assigned to anything important.
• Mana regeneration is inadequate.
• Current implementation of shards is primitive.

Suggested changes. (those should not be separated and will only work well together)

1. Reap the essence apart from maximum mana. Essence is better off playing a role of "wish points".
2. Let maximum mana be based on wisdom.
3. Split mana into types one for each shard and one "independent".
4. Allow shards to have multiple types to choose from. Let them increase Regeneration of associated mana types.
5. Introduce "Mana beacons" let them handle summoning limits and independent mana regeneration.

Detailed explanation. (along with some optional additions, most of that can be reaped out and the system will still work. I trust in Stardock's ability to understand which ones can and which ones can not)

1. Essence.

• Give every initial sovereign same starting essence. "Quest" sovereigns aka dedicated spouses start with small amount of essence.
• Let it be used to create resource nodes.
  • Only one forth of total essence can be spent that way.
  • Essence that left the world permanently does not count towards total essence.
  • Essence that still exists in the world as extension of sovereign counts towards total essence of that sovereign.
  • Essence consumed by another sovereign does not count towards total essence of original sovereign. It now counts towards total of sovereign that consumed it.
  • Resource nodes are permanent. They can not be destroyed/dispelled/consumed. They can still be used by other factions should they take a hold over them.
• Let it be used to imbue champions with mana and casting ability.
  • Only small amount of essence is taken and is only used to enable spell casting.
  • Champion's spell casting is determined by his stats in the same way as sovereigns.
  • Champions CAN NOT use strategic spells.
  • Champions poses every tactical spell in the arsenal of sovereign that imbued them with essence.
  • Sovereign can recall part of his essence back from the champion. The rest of it is permanently lost. And champion loses his magical abilities (but keeps his int. and wis. scores).
  • When champion gets killed by sovereign small part of his essence transfers to that sovereign. There's a small chance of that sovereign inheriting a random spell from champion's arsenal.
  • Recall champion brings champion back without any magical ability.
  • The idea here is that champion is a conduit for sovereign's power (any remainders of Mass Effect are unintentional, except the one which resulted from me naming it).
  • For fun's sake make familiar act the same way except for essence parts.
• When sovereign marries another sovereign. Small amount essence is consumed from both sovereigns. Their off springs inherits essence of both their parents and is himself/herself a sovereign.
  • Every offspring of that couple then starts with the same amount of essence as the sum of essence taken during marriage.
  • When a sovereign is born (s)he randomly inherits some spells from both of his parents.
  • Every sovereign can cast both strategic and tactical spells as long as (s)he has knowledge of such spells and required spellbooks. This ability is retained even if there's no essence left to spend.
• When sovereign marries a champion (s)he retains all his/her essence. Only champions are born from that union.
• Two champions do not produce offspring worthy of notice.
• Sovereign can choose to transfer some of his/her essence down the line of succession. This transfer is irreversible and no spell knowledge is transfered along with it.
• When a sovereign loses a battle (s)he loses part of his essence. If there is no essence left to lose the sovereign dies.
  • If no sovereign was present in defeating force then all that essence is lost permanently.
  • If (s)he was defeated by another sovereign, that sovereign absorbs part of that essence. The rest is lost permanently. There is a small chance of that sovereign inheriting a spell form defeated sovereign's arsenal.
  • If (s)he manages to escape alive (s)he retains the rest of his/her essence.
  • If (s)he dies the rest of his/her essence is automatically transfered to his/her direct successor (Aka first in line for the throne. Sovereigns not belonging to the same kingdom/empire are excluded.)
• Summoning does not cost any essence. It is limited only by available shards, beacons and mana.

2. Maximum mana.

• Only creatures capable of spellcasting have mana.
• The size of mana pool is based on current wisdom of the caster. Regardless of amount of possessed essence.
• Every alteration of characters wisdom also affects the size of his mana pool.

3. Mana types.

• Mana pool is split by types.
• Various spells need different types of mana.
• More than one type of mana may be needed to cast a spell.
• The cost in every particular mana type has to be taken from mana pool of that type. Cost don't have to be equal - Some spells may be more taxing on one mana type than on another.

4. Shards.

• A single shard may contain several types of mana.
• A shard can be more effective for one type of mana than for another. (I recommend fluctuations between -30% and +30%)
• When harvesting a shard player has to choose which mana type to harvest from the shard.
• Late game upgrades may allow to harvest a second type of mana from the same shard or to harvest more mana if the shard only contains a single type of mana.
• Some spells need certain number of controled shards attuned to specific mana types. More than one type of shard may be needed.
• Shards replenish mana pools of the type they are attuned for for every spellcaster in kingdom/empire on daily basis.
• Amount replenished depends on effectiveness of shards with the type they were attuned for.
• Regardless of existence of shards every spellcaster possesses every type of mana and replenishes at least minimal amount of mana of every type every turn.

5. Independent mana.

• There's a type of mana not associated with any shard.
• It it is attracted by mana beacons and can be harvested using them.
• Mana beacons can be constructed in settlements of hight enough level.
• Only one beacon can be constructed per settlement.
• Mana beacons replenish independent mana pool for every spellcaster in kingdom/empire on a daily basis.
• Regardless of existence of beacons every spellcaster possesses independent mama and replenishes at least minial amount of it every turn.
• Mana beacons also serve binding function allowing summoned creatures to remain under control of their summoner.
• The more beacons kingdom/empire has available the more creatures can be controlled by the summoners of that empire/kingdom.
• Some creatures may be harder to control than others.
• If at any moment kingdom/empire does not have available amount of beacons required to control all the creatures it's summoners have summoned creatures start randomly escaping control and going berserk until there is enough beacons to take control of all creatures that have not yet gone berserk.
• If at any moment kingdom/empire does not have available selection of shards required to summon any particular creature it's summoners are attempting to control, such creature escapes control and either vanishes or goes berserk.
• Late game upgrades may allow stronger beacons that replenish more independent mana and offer easier control over summoned creatures.
• Familiar does not share the same mechanic as other summons.
  • It does not need a shrine.
  • It shares HP pool with it's master but does not share mana pool with him/her. Damage/healing dealt to one leads to damage/healing being dealt to another. Death of one leads to death of another.
  • There may be more than one type of familiar.
  • Familiar can be freely summoned and unsummoned.
  • Familiar can only be summoned by original sovereign or his closest successor (the one that inherits his essence) in case the original sovereign is dead. Only one familiar can be summoned at any given time by any given sovereign.
  • If at any time kingdom/empire does not have available selection of shards required for summoning of currently summoned familiar, familiar is unsumoned.

Some suggested spells to go along with suggested system. (pretty much everything here can be safely reaped out)

• Mana transforming spells allowing to transform one or more type of mana into another type of mana or several other types of mana at reduced rates.
• Mana transferring spells allowing to transfer mana from one caster to another at reduced rates. (this is meant to be strategic spell unavailable to champions (well maybe as an exception make it available to familiar)
• Resource node creation spells. (have to take essence)
• Resource node corrupting spells (dispellable enchantments only) (don't require essence)
• Different familiars to chose from. (don't need to much diversity 3-5 types tops with different tiers for each type) (don't require essence).
• Summonable artifacts. Something like "astral blade" or "plate mail of elements" very strong, use beacon limit, for obvious reasons don't go berserk - simply get unsummoned.
• Summonable mounts! Sorry, just had to say that . In fact I'm kidding on this one. Although i guess it is an option and mechanics would pretty much the same as with artifacts, since mounts are just equipment.
• Even more landscape altering spells. (including volcanoes earthquakes and other disasters, also need something to get things back to normal after them) Those are cool.
• More divination spells (like seeing your enemy's kingdom/empire details or what research (s)he has).
• Ahem, healing spells. (strategic mode only)
• Err... killing spells? No... I guess we have those already...

Phew... I guess that's it...

[Idea geyser hits you for 25 points of damage in the eyes and induces sleep effect]