Loving this mod pack so far. Seems to play nicely with the various other interesting mods I've found as well. That said, I've run into a few issues that you may have already addressed, or that are limitations of the game itself.
Kingdom Paladins can fail their Bonded Mount quest by not casting the spell near a Swamp, then selecting the Spirit Warg choice. This appears to be because the goodie hut for it is limited to swamp terrain, so if there isn't one in range it doesn't spawn.
Various terraforming favor values don't match up with their descriptions.
Sorcerors and Paladins feel kind of overpowered compared to vanilla classes. Especially, every level trait for them seems to me to grant significantly higher bonuses, combined with much greater synergy, than those of almost all vanilla class traits. Granted, they seem to fit thematically, but the combination of significant skill synergy and generally faster leveling potential (XP bonuses on solo Paladins, passive leveling spells on Sorcerers) feel like they ramp up to game-winning levels of power very rapidly. This may just be that most vanilla classes are on the underpowered side, though.
If you take over a Dagoroth outpost, it continues generating its resource. However, you can't use it, and it clutters up the bar. Is there a way to get rid of it?
Republics can't construct the wonders that upgrade from an existing improvement. Only really noticed this with the Treasury Vault. Granted though, they really don't need it, they already have ridiculously strong economies by that point in the game.
Using the spell from the second Master Quest that takes control of another unit on an enemy Sovereign can lead to all kinds of strange results. May or may not be in combination to then accepting the surrender of said Sovereign. Basically, I got my own Sov permanently immobilized by swiping an enemy Sov from a city in which they were recuperating from a previous defeat, then forcing their surrender.
Favor-requiring tactical spells get stuck in your hotkey bar in tactical battles if you lack the favor to cast them. You can't overwrite them with another spell.
Sorcerer resource-summoning spells can trigger on top of rivers. Same applies to the seed from the Life Favor gift spell.
Some swords aren't registering as swords for the purposes of Paladin traits/skills. Notably, the Searingray Edge from the Terraforming module.
Procerpine's crown seems to be negating the Fame upkeep and Metal upkeep of the Sorcerer enchantments as well as the standard mana upkeeps. Not sure if this is intended or not, but if it isn't, perhaps it's possible to change by moving the upkeep into the effect applied to the unit rather than using the standard SpellResourceCost?
Sorcerers' +1 casting times seems to be applying to all combat abilities that aren't a basic melee attack, including bow shots, staff shots, etc. Not sure if this can be, or even should be, changed, but it's worth mentioning.
I think that's just about everything that comes to mind. I know it might feel like I'm complaining, but really, you've done a great job, and I'm loving the overall experience. Looking forward to the next version!