HOLY CRAP! Significant improvement!! I'm lovin' the work guys. I was finally getting that "Just-one-more-turn" fever, the depth added by simply the different damage types compels me to really investigate who I'm attacking and who is around me in the world. I carry a couple different weapons with me in case I need to switch something out. I feel I have to weigh my choices ever more carefully... and I like that. 
The List:
When hitting ESC at the CityLevelUp screen to adjust a game setting, upon returning to game I lost the screen and the ability to choose. Checked, and no building had been chosen for me either.
[Typo] Mason: At CityLevelUp screen, Hover-over tool-tip tells me that this building decreases building costs by 10%. When I click that option from the screen and the box below the building option that shows me a sample image tells me that this building increases production by 10% when constructing buildings. Not sure which is true yet!
On UnitLevelUp screen, some new (already active) traits do not show info when hovering over them. See below:

When equipping my unit and checking on unit's encumberence via mouse-over, will tell me "Encumberence: Light" but not "Encumberence: Medium" when between 60-80% loaded
-- Also, seems ambiguous that "Light" is defined as less-than 50% (inclusive) but the next increment of Encumberence does not begin until 60%.
Should say in spellbook that Enchanted Hammers has upkeep of 1 mana / turn
While moving to a location to complete a quest, I was attacked by a bear. While in the tactical screen, I wanted to bring up the bear's stats and compare them with my own. When I clicked the image of my sovereign to double-check their stats, it brought up the quest's finishing screen and my sov leveled up.... the rest of the battle was very buggy. Almost crashed the game. Was pretty hilarious, though. See below:

On the initial quest screen where it now tells you what your reward is, it would be really nice to be able to mouse over something new to you like "Regeneration Potion" to know if it's worth hunting around for!
-- Also, on the Snake Oil quest, it tells me the reward is "A Random Magical Item" but I get 80 gold instead. Was I fooled intentionally on your part, Stardock? 
And just a balance issue: On the whole, I think the 10% sell-back value for items is a great way of reigning in the scale of things, but it also makes purchasing new items at full-value incredibly difficult and much less lucrative of a deal vs. designing a new unit and training that... undermines the ability to purchase items in general. Suggestion: Instead of reducing sell-back value dramatically, scale back the value of everything and return sell-back value to 50%.