Alright so I have played through several times now, and have a list of praises, grievances, and bugs to air.
Balance and Tech
As everyone else has said basic infantry are too weak in comparison to champions. Firstly they die too easily. They need a hp boost and their members need to die less, the dmg drop is painful. Members of squads should only start dying once their hp has dropped past half, not right away. You could also have a anti overkill ability were a single attack from a single champion will only do full dmg to the first unit in a squad it kills and the dmg is reduced for each unit in turn, so that champions can't instagib entire squads. That may be too complicated though. The main thing is that champions, especially sovereigns, have to much health, and troops have too little and taking even little dmg will greatly reduce their dmg. Troops also need the cost of upgrading greatly reduced and the ability to upgrade their squad size.
Research is a bit too slow. This causes champions to level up much faster then the rest of the game because they don't need techs to raid lairs and farm monsters. A small reduction would help this, say 10-15%. The other thing that reeaallyy slows tech research down is the two tier gap in tech research tree. You can't have increasing tech costs but not increasing ability to research, or you will stall hard. Either add another research building and tech to the civics tree or better yet to the magic tree.
The magic tree could really use love, it's mostly useless. Tech is and always will be, disregarding champion cheese, the most important resource. If you make the civics tree the only way to get it then you are forcing everyone to focus on civics. So add a 3-4 tier research building to the magic tree, make it require crystals or consume mana or something. Or better yet since magic and champions are tied together maybe make a building that takes a garrisoned champion's intelligence and turns it into research. Hell add more then one magic research building. Reward players for choosing to invest in the magic tree by letting them be better at researching even more magic stuff, if you don't it will always be secondary to civics and everyone will use the same strategy.
The same goes to a lesser extent for the military tree. Maybe add a tech that generates research by conquering cities and killing enemies. Or that gives a small research boost in garrisoned cities.
I have never bothered to even really look at unrest. Has anybody?
Maul is still broken when used by high accuracy champions. Cheese.
Champions need a xp curve as well. Once you hit lv10 or so your leveling should drop dramatically. Low level monsters and normal troops should stop giving xp after around level 10 as well. So you can't farm stupid units you can 1-hit KO. Also as other people have said champions should not share xp from combat, it should be split. Otherwise you end up with a mob of champions. Troops however should share xp.
Way to many abilities, items, spells, and traits give movement. It is broken. Units should not be getting like 10 tactical movement. Mounts should also not stack with boots. Once you get mounts they are also way overused. There needs to be earlier game counters to them so they don't get overused. Also champions should require a trait to use mounts, and another to use exotic mounts. As it stands there is no reason not to just buy mounts for every single champion.
Bows are too weak and hard to get. I haven't seen any magic ones yet. More bow traits for champions are also required.
After taking cities their population was reduced to zero.
Mass Spells can't fail.
The cursor is still not right, it doesn't always transform correctly.
A lot of quests still give rewards when you flee from the monsters.
A lot of units seem to think they are air elements and whoosh around. Caused by haste being cast in combat?
My research bar was completely covered by the tax bar late game.
Animations for special attacks when you use a bow are odd... Why so they spin and wave the bow around? lol