First and foremost, this is a HUGE step up with several significant advances.  Well done!

A few things:

- New weapon skills are amazing, adding a lot of tactical depth.  I want to use them more.  Suggestion: lower the cooldowns.

- The faction skills are in the same boat, mostly.  Soul Spark doesn't feel right to me.  15 mana for ~5 damage is pretty weak.  Suggestion: this looks like it'd be a great spam skill: make it cost 3-5 mana, 0-2 turn cooldown, 1 damage/level, remove the "per unit in a group" multiplier

- The hero skill trees are an amazing addition, my only gripe is there are too many passive stat bonuses and too few active abilities.   Taking 5 levels worth of Leathality or Evoker is kinda dull.  Also most of the stuff in the "general" tree is kinda weak.  Suggestion: more active skills, or more strategic decisions (+5 strength and -5 HP kind of trades).

- I made my Sov a mage and she was pretty gimped early game.  I didn't have enough mana to cast a lot of spells and couldn't risk putting her on the front lines so she just kind of sat in the rear and watched.  Suggestion: make some kind of magical ranged weapon available for Sov creation, like a wand or staff.  A cheaper Soul Spark could fix this for Paradin.

Bugs:

- pathing is a little off.  I sent a pioneer 2 squares away, across a river.  If she crossed the river it would have taken 2 turns but she insisted on going around it, taking 4.  

- Army stalling.  I sent my army somewhere across the map, hit next turn a few times, realized the army hadn't moved at all.  It might have been confused by crossing city borders?

- Berserk units still cast spells.

- I lose a ton of mana whenever I use auto-battle, this intended?

Edit: playing as Quendar ATM, and Flame Tongue is weak.  Suggestion: level x3 dmg, maybe set things on fire, or give it a spread like Burning Hands