First I'd like to say that I've been playing this beta from 0.912 to 0.915, and the improvement over such a small time is staggering.  Really looking forward to Beta 4.  Anyways, just finished up a Quest win on Resoln on hard with the latest patch, and felt I should contribute my thoughts.

Interface and General Gameplay

Interface
- For the research bar at the top left of the screen, it currently displays the amount of research, and if you mouse over your selection, it shows the time left.  Personally, I'd like this to be reversed.  Amount of research I don't really care about while playing, but the length of time until my tech does.  So it should show the time left all the time, and mouse over for research amount.

- The tax slider currently shows, upon hovering over the change arrow, how much your values of various things will be. (tax income, unrest, etc)  It also changes color based on the type of change (same, lower, higher).  I'd like the interface to show how much it changes, perhaps in brackets.  I find myself hovering back and forth trying to figure this out whenever I go to change it, and it is annoying.

- Spellbook interface is frustrating.  As a method to sort spells, I find alphabetical to be poor, since I rarely remember the exact name of spells.  For both tactical and strategic spellbooks I'd rather have some other method of sorting.  Perhaps by type of magic level needed (Air, Earth, Research, ..) or type of effect (unit buff, unit debuff, damage spell, city buff, etc.).  I find this much easier, as I remember the effect of say aura of grace(city buff to trained units) then the actual name.

- On the topic of spellbooks, it could use a tab system for the strategic spellbook, since by the end you get so many.

- Spells cast on cities should show up in the map view, ideally.  Late game I spend a lot of time here, and keeping track of buffs is annoying having to zoom in.

- Setting waypoints from generators or cities would be great.  Having spawn day for my binding summons at the same time my ogres came gave me about 15 units at once I had to send to various cities every once in a while, and it took forever.

- It is very difficult to tell if you've lowered enough ground to move through a mountain.

- I'd like an easier way to see every spell of each school.

Gameplay

- I dislike the narrow, deep tech trees.  They don't allow much customization intra-path customization, and only a little inter-path choice.  Between the steep cost increase as you go down the tree, and the interlocking requirements, there is little ability to rush specific techs for a situational advantage.  For an example, I was excited this game because I found a bunch of ogre lairs early game.  But because they are quite deep in the civ tree, I have to have virtually every civ tech unlocked to that point to get them.  But since rushing down the civ tree alone isn't really an option, I had to just wait until I'd cleared much of the tech trees before I could get wildland allies.  Admittedly, if I'd had my ogres right away it would've been unfair.

- There seems to be a 3 turn limit for making new units.  I really dislike this, as it means my forge cities can't pump out men quickly.  My favorite tactic in any game is a swarm of expendable men, but when a significant number of my cities can't produce men with with sticks faster then knights this strategy falls flat.  Resource costs seem like they should help, but I haven't found them that steep to make me focus on not elite troops.  I'd like to see the limit being 1 turn for troops, 3 turns for pioneers.  If I had to guess why this limit is in place, I'd say it is to avoid people spamming pioneers everywhere, and swarming the map with single unit stacks for a human locust wave.

- AI targeting in combat could be more intelligent.  Spiders webbing archers, enemy mages casting berserk when they have 1 hitpoint left.  The only reason the enemy AI is ever a threat is the huge number they get through their economic bonuses.  Of course I imagine this area will see a lot of work.

- Traits are my favorite thing about customizing my guys.  I'd love more of them, that are contextual based on equipment and race.  There has already been some of this, with the last patch.  What I'd really like to see, however, are traits based on weapons.  Right now basic soldiers are somewhat bland.  You really just move and attack, or maybe throw some knifes.  So just some suggestions:

Name/Requirements/Effect

Hamstring/spear, sword, or dagger, encumbrance under 50/once per fight, can immobilize on hit

Momentum/mounted/can move through non large enemies, instead of making an attack, every enemy moved over takes 1/2 attack damage

Pike Formation/spear weapon/as an action, instead of attacking, you gain one counter attack.

I'll stop here, but I could spend all night coming up with these.  Obviously they are more work, and difficult to balance, but I think it would add a lot to unit design.