So, I've been mulling this over for a while now, and am finally ready to put some concrete ideas out there on the matter.
We are supposed to have the capacity to use one or two huge cities as effectively as a horde of lesser cities as a compelling game play option. The implementation of some cooler high-end buildings, the recent changes in population, and the new gold taxation stuff all go a long way to making this balance out. The one thing that we still have quite literally preventing us from having the capacity to do a 1-2 city game is the dispersion of strategic resources.
Reasons as follows:
Food: At present, it takes at BARE MINIMUM two fields to get one city to level 5. Simply by building a second city, you slow that down. By making that second city level 2 to make it useful, you slow it down further, and perhaps even make it require a third city at another food source.
Metals: Late game, this stuff is where it's at for military units. Most games, by the time I locate and exploit an Iron Mine, I'm already swimming in so much basic materials from my workshops that it makes me want to set all my cities on fire so I don't have to store them any more. If you happen to get unlucky enough to be denied Iron, it's pretty well game over for you.
Crystals: Also, late game magic goodness. This stuff is less hard to find than Iron in my experience, but still requires a bit of luck.
Shards; You start with one. You will probably have a second within maximum prestige range of your capital. If you get REALLY stupid lucky, you might get a third. Any chump with 7 outposts can have more access to mana per turn than you do.
All of these seem like pretty significant late-game stumbling blocks for those who want to do a "Sauron-esque" single city game play style. Or alternately, if you get really unlucky with an Iron Mine and have to fight people in plate mail with wood spears (or are trying to develop and cant physically get to a second source of Food).
I propose a reconsideration of Essence as originally intended for a second type of magic. "Creation".
Bear with me here; The original concept of sovereigns was to have a finite source of magic which could be used to do awesome stuff. They could either horde it to themselves, or spread it around and diminish. We never really saw it implemented well. In fact, I argued against its implementation, but feel that it has a place in making this game direction great. Let me define the uses.
What you can do with Essence:
-Pull fertile soil from the ground for farms
-Pull resources from the ground
-Imbue other casters with the ability to use spells
-Create puissant artifacts which can be given to your champions
-Subvert a developed shard to your control, despite its previous owner.
-Kept to yourself to maximize your own magic's effectiveness.
Implementation;
-Your essence equals 10. No way to raise or modify it.
-There is no way to ever increase your essence.
-All essence spent is permanent, excepting imbued champions, from which you may regain your essence when they die.
-All sovereigns develop the ability to put essence to use as they level. (You're level 3 now? Here are your Essence spells)
-Essence Spells cost 1-2 to cast. Perhaps higher costs for creating mighty artifacts.
-Essence determines how fast you cast spells (once the variable initative is implemented), and how many mana points you may spend in one turn.
-All damage-dealing spells in the other lores get a modifier of [(Spell Damage+Shard Effect+Int Modifier)*(Essence/10)]. That means you spend 1 point of essence, and all your spells will permanently be 10% less effective as they once were, but you have a permanent and enduring benefit to your civilization (new fields, a second caster, so forth)
-At less than 5 Essence, your spells become easier to resist. As I'm not sure what the current resist mechanic actually is, I have no ideas on how to implement this feature.
-Those who are imbued with the ability to use magic are treated as having an essence of 6 for purposes of damage/resist. This keeps you very powerful as compared to other casters unless you make a lot of casters, in which case, you are better served as a figurehead in your city with hordes of lesser mages running about.