Summary: 

Magic sovereigns need additional capabilities to allow them to compete with warrior sovereigns. Limiting high level spell use to sovereigns that choose to focus on magic would go a long way to making them stand out. Adding early access to some spells would help them compete in the early game, and a tactical mana pool or having magic ignore armor would go a long way to ensuring that they remain fearsome opponents all the way to the endgame.

Issues: 

Mage sovereigns are underpowered relative to combat sovereigns in practically every way, at every phase of gameplay

Mage sovereigns have no advantage over mage champs

Mage sovereigns are required to utilize a heavily limited global pool to be minimally effective in combat

Spell based combat requires two global resources (mana pool and research points) for use. Combat requires only one (research points).

Solutions:

Limit level five spells to sovereigns who choose a magic trait (call it something like Attuned or Magical or Chronic Wizardhatter). This trait should reduce the physical damage output of the sovereign that selects it to penalize players who build a warrior sov and select the trait to retain l5 spell access.

Allow mage sovereigns to select two or three level 1 spells that start the game researched.

Give magic focused sovereigns a personal tactical battle mana pool that does not drain the global pool OR make spell damage ignore armor.

Explanation: 

Magic is expensive to use, and even more expensive to develop, but provides little or no advantage in combat relative to a well armed sovereign with good armor. Furthermore, magical capability is entirely dependent on empire size and shard acquisition rather than the sovereign xerself. Meaning if a player decides to play as a mage, they are entirely dependent on the vagaries of the map generator and their ability to acquire territory through settlement or force of arms. A physical sovereign or champion with access to more shards is as effective, or even more effective, than a high int sovereign at combat casting. This is irritating!

Limiting level five spell access gives players who choose to have a less capable early game sovereign something to look forward to in the late game. It also gives them a reason to focus more heavily on magical research since it only pays off if you develop heavily.

Mages are further limited by their inability to cast any spells whatsoever at game start. If they choose to forgo economic or military research and also dedicate a secondary city (or city slots) to magic research, they must still wait several turns to pay for a single low damage spell. Hitting someone with a sword has no comparable cost, and requires zero early game investment. In terms of damage per turn (DPT) or damage per combat (DPC), it's not even close.

This requires two solutions. First, sovereigns who choose to focus on magic should be allowed to start the game with a couple of spells for immediate use. This would give them a leg up in comparison to their beefier brethren. They'd still have to set up an arcane research city and go whole hog on shard grabbing, but at least they wouldn't start the game with nothing to show for their lack of physical capability. They'd still be losing on DP* comparisons, so this should be used in conjunction with one of the two tactical combat options.

A personal tactical mana pool for mage sovereigns that regenerated faster than the global pool (or even regenerated completely at the end of combat) would go a long way to rectifying the DP*. And since the pool would only be accessible to the sov and only in tactical combat, they wouldn't be able to engage in most obvious exploits (eg casting through a summon or something equally silly).  

Alternatively, allowing spells to ignore armor would make magic competitive in the late game, when armor can completely eliminate magical damage. A plate armor wearing army can shrug off magical damage while obliterating the opposing side with high tech weapons. It'd have the added benefit of ensuring that low level combat spells are still useful in the late game. This should not be used with a sov specific tactical mana pool, for obvious reasons!