This game is a hybrid between RPG and TBS. Perfectly matching the power of the two is very difficult and for people just trying to win rather then "enjoy the ride" (something that is unlikely to happen unless significant sandbox elements are introduced) choosing to use the one (TBS or RPG) that is more powerful (RPG) as a path to victory just makes sense. I believe that the lore supports the RPG element being the more powerful one and I see no issue here.
So there is nothing wrong with super sovs... in fact its the main theme of the game. This is like skyrim only instead of smiting to get the best gear in the game you use TBS aspects to get +mana and buying items and upgrading your city shops.
And frankly it would be greatly more enjoyable if it stops being so damn coy about what it is and starts properly fleshing out the RPG side of things which is currently way underdeveloped and lacking in polish compared to the TBS aspect.
So please flesh out the RPG (dominant) portion of the game!
Now... if it just so happens you want the TBS portion to be major, either balanced or the primary aspect of the game then one tiny change is needed. You need to remove the stupid "it takes 3 turns minimum to build anything" rule... allowing MULTIPLE things to be built in a single season as long as you have the hammers. And in addition to that, you should drastically lower cost of structures.
Cities will then be able to finish construction and spend turns building armies.
At the moment building armies means not building +mana, +gold, or +research buildings all of which empower your super sov. But if your cities are sitting idle having already maxed on their sov bonuses then there is no reason to not start building armies. And once you have the armies you might actually put them to use. And suddenly this is a balanced hybrid.