NPCs. Playing as a Trog today makes me uncertain why an NPC from the race of men would want to sign on board. Should they just cost more? Or should they be hostile? Or what?
Interesting Choices. Being forced to spend essence to build a city is not a choice interesting or not. I’m inclined to find some other use to revive land rather than forcing users to use it to effectively build a town. That is, we’d let the player build cities on the foresaken land. That’s a pretty big game change but when you add the new game behavior that the sovereign can only found their kingdom (after that, only pioneers can build cities) it makes things a lot more fun. I’d rather see essence used to generate fertile land or something (as an example).
Well, technically, it only forces essence to build a city that's not on "green land". This is actually good, since it prevents rapid resource grabs. How will it work if you remove essense cost and give only pioneers the ability to settle after the first city? Will they still need green land to settle? If so, then you've just made it more cumbersome since you'd still need a Sovereign to go there and revive the land, but now you'd also need a pioneer trailing him to settle the city. If you don't require green land for city, you open it up to fairly quick resource grabs (yes, I realize pioneers cost a lot but essence cost of founding a city trumps resource costs). Especially players who take a faction that gets bonus resources at start can get this going pretty quick. Basically, requiring essence to build a city off "green" land serves a pretty important purpose of making player expansion a bit more natural, rather than scouting all the juicy places on the map and putting a city down at each. Please account for that when you're re-designing this behavior!
NPCs. Playing as a Trog today makes me uncertain why an NPC from the race of men would want to sign on board. Should they just cost more? Or should they be hostile? Or what?
Well, if there are "men" NPCs wandering around, it would make sense to have "fallen" NPCs wandering around too. In this case, recruiting them could require magic, but offset by the unique bonuses they may provide. For example, Men have their Merchant NPC that generates gold. Now, I can't quite picture a Trog merchant so it would definitely make sense if Fallen didn't actually have any Merchant NPCs. So, say, instead of making a deal for gold, what if cross-race NPCs required a maintained Charm spell? Essentially, they would be hostile until you charm them, at which point they join you, for no gold cost. Since Charm would be a maintained spell, they would go hostile and leave you if you ever stop maintaining, and since there will be a limit on number of spells to maintain, that should be enough of a "cost" to not require gold for them. It would also mean some more interesting choices for the player, if he wants to maintain more buffs on his army or maintain charms on unique NPCs that provide otherwise unavailable bonuses. Logical gameplay choices are great. 
Quests. I’m inclined to have quests have an Allegiance tag. That is, Empires would get different quests than Kingdoms. Right now, they share them. Relias, the do-gooder might escort some princeling to his estate. Verga, however, would use his bones as a paste.
I could see some quests being different, but not all. For example, this morning I found some ruin with writing on the wall that led me to some tomb with a demon. This kind of quest is pretty neutral, not requiring any character interaction, so should be available to both races. But those quests you get by walking into an inn.. well, "A wraith walks into an inn....". Let's just say humans probably won't be quick to ask it to escort their kid *anywhere*. On the note on quests, it'd be great to have more than just the "good" and "evil" ways of completing quests where such choices are presented. You can only ever either let the Dark Wizard go and take his money, or kill him. Help the wolf give birth, or kill it. Get the Knight's sword from the bandits, or take their money and let them go. These are boring choices. It would be fantastic if, for example, your quest doer's Charisma stat opened up more inbetween options - think D&D dialogue where you can Intimidate or Persuade. So instead of killing bandits for the sword, you can threaten them so much that they give you the sword, money, and run away screaming in fear. 
Spells. Need a LOT more default spells that you can learn.
Well, it should be a bit more indirect. Give all the different spell books more low-end spells, so a Sovereign that's more focused on Magic will have a wider spell choice selection, but someone who just goes with the Basic will still have just the necessary essentials.
Spells #2. Need some way to queue up spell learning.
Maybe, maybe not. Notification that you have the max spell points would be great so you don't lose production because you're capped. But you'd have to give the player control over the queue, which more or less means they'd be spending the same amount of time in the spells window, just more upfront to throw them in the queue. As for how to implement it? In the Spells window, make 3 (or however many) empty circles and label them something intuitive ("Spell research queue" or something). Clicking on a spell in the book adds it to the queue (FIFO). As soon as there are enough spell points for the top queued spell, it gets learned and the rest of the queue moves up. Clicking on a queued spell removes it from queue. Can do more fancy stuff such as if you have 3 queue slots and 1, 2 are taken and 3rd is empty, if you drag a spell from the book over 1, it becomes 1 and the existing two spells in queue get shifted to 2 and 3.
City Improvements. I’d rather see fewer general improvements and more 1 per faction (Imperial Achievement) and 1 per world (World Achievement) buildings so that specializing cities is more fun.
With fewer improvements you'd need to drop the number of build space available. Cities aren't just unspecialized because there aren't any 1 per faction or 1 per world improvements, but because you can build basically everything in every city and there's never a reason not to. There have to be more improvements than build space so if you really want to make a city into a military training city, you sacrifice gold production or food production in it almost entirely. Or if the city is in a food sweet spot, there would be very little room left for anything else, so on. Basically, it has to be balanced such that there are enough improvements for every main city "function" that doing it prevents expanding the city's other functions to their entirety.