I've visited this forum from day one, and been in the previous beta as well, but haven't had time to test much. My background is in Human Computer Interaction, and user interface design, so I tend to be somewhat analytical in my impressions. Also, since developers will become very familiar with their software with time, I'm writing this from a perspective of a first time user, focusing on intuitivity pitfalls that I've come across.

Here we go:

* You can't click anywhere (or outside of) the book that first pop up in a game. You have to locate an itsy bitsy rather difficult to see X and aim for that in order to close it.
Fixed in Beta 4!

* Scrolling the view by moving the cursor to the window edge is extremely slow.
Fixed in Beta 4!

* Scrolling the view by arrow keys is also extremely slow.
In Beta 4, the arrow keys moves your active unit. I would prefer to scroll the view, but that is a personal opinion.

* Grey objects seem to indicate fog of war. But having even a small city with no units being partially fogged at the edges seem rather silly. The peasants aren't keeping an eye out in these dangerous lands? Even if they are sleeping through the day, it just looks weird.
Fixed in Beta 4!

* It took me a while to figure out why I couldn't build a hut. The red number could be made stronger... perhaps encircled or with an outline. More importantly, the tooltip popup should say "food shortage" or "requires 2 more food than you currently have", instead of just "food" which doesn't explain much.
In Beta 4, nothing has changed for this but I'm crossing it out anyway because this is one of those things that "you only need to get it explained to you once, and then you will understand it".

* I can't see a button for moving to the next available unit (that has moves left this turn).

* I can't see a button for having a unit continuing the orders from the last turn.

* Actually, just having a target marker for a unit's move order is not enough as it can be hard to see, especially if it is far off (out of the screen perhaps). I would like to suggest a dashed line indicating the full path of travel in addition to the target square.

* I have found no icon for trash/ground to dispose of items (right-clicking also did nothing). It's needed because unless I'm mistaken, the starter item is a useless item? Several games in a row, the first item I found was a dagger and so I wanted to get rid of the starter item.

* There is little (no?) indication of when a new turn starts after you press the next turn button. This is especially obvious early in the game when perhaps there are no other movements or such on the map that you have to wait for. I would perhaps suggest a box saying "turn 23 has begun" at the top middle of the screen which fades away when you move the mouse, accompanied by a sound in case you are away from the computer.

* I now see that there a symbols for events along the right of the screen. This is fine for experienced users, but for first time users, I think it would be more informative to have those symbols at the top middle of the screen along with explanatory text which can then fade away or be put to the right (as a toggle perhaps, for those who want more, or less information regarding what's going on).

* The button for moving a unit out of a settlement is equally as small as the X to close the book... but proportionally much larger to the area it is attached to, and also very close to the cursor when it appear, so it might be OK... but it could be better.

* The text explaining essentially to harvest special location X by harvesting special location X could possibly be changed to "automatically harvested" or "no research needed to harvest"... unless I misunderstood the text, which either way is not a good thing.

* There is currently quite a lot of red text (numbers) on brown background. Not sure if color blind people will have issue with this, but visually impaired people might as the contrast between the hues is quite low (I'm not, and I'm still bothered by it). I would suggest changing the background color or adding an outline or drop shadow to make the red text pop more.

* Hmm... lots of new very small buttons in a lot of places... but I read that the interface was going to get an overhaul, so I won't point out everywhere they are used.

* Heroes wandering around changes my cursor to a speech bubble that is crossed out. That is counter-intuitive in two ways: 1) the game does not tell me why it's crossed out (even when I'm next to the hero and should be able to talk to them) and 2) it should never be crossed out at all unless they are hostile, rather use a speech bubble with a pair of footprints next to it to indicate that your sovereign will chase after the hero to try to speak to him/her if you click.
Fixed in Beta 4!

* There's a bar saying "civilisation: in 15 turns", which apart from being a weird use of colon should be reflected in the corresponding bar in cities, saying something like "city progress in 15 turns". Right now, you're left guessing as to when the city will develop to the next level.
Brilliantly fixed in Beta 4! 

* Reading from books directly via the inventory tab just makes them disappear. No message regarding what happened, or even a small glowy animation to direct the user's eyes towards any change.

* The game tells me that mills generate 2 building materials. Is that per turn or a one time thing? I'm confused, because they appear to take shorter time to construct than workshops, which only generates one building material...

* I don't play each version much because I don't have time, but I could have sworn that I got messages in a little banner at the middle of the screen before when a building was finished in a city. There needs to be an indication when a city's build queue is empty.

* Sword as a symbol for dealing damage seems to exclude magical damage. How about an explosion instead? Also, a heart as a symbol for damage taken seems to exclude healing as a stat on there, so how about a drop of blood or three instead? The crown for experience also seems like a stretch... will they all become royalty? I would suggest a medal as a symbol for that instead, which is something more commonly used in games for this kind of thing anyway.

* It took me quite some time to find the movement symbol and stat in combat. That icon, and also the cursor for movement, is very busy (what does the color green mean in the icon? grass? what if you are on a mountain or in desert?). Also, I guess different terrains have different movement costs, so it would be very nice to be able to see that movement cost directly on your cursor, so you can plan a bit before you move.

* Is there a gameplay reason for leaving the characters by the edge of the grid after they have attacked? If not, it looks odd and the grids could be mistaken for empty grids if you don't watch carefully.

* I though that the red ring around the city icon at the top left corner of the screen was a timer for when the build queue was complete, but that does not appear to be the case. I'm not at a total loss as to how to see which cities are currently building or not.

* I was sent to clear out rats in some ruins, but I must have missed the danger level indicator because when I clicked on the ruins I found myself immediately in battle. I also don't think there was any pre-combat screen as with wandering encounters, which is bad inconsistency. Then, for some reason, my sovereign announced that he had gotten hurt and retreated (without me seeing the battle) and yet I got a message that the quest was complete. There was no post-battle screen either, so all in all, a very confusing experience!
In Beta 4, the rats weren't even a combat situation, just an event text (rather disappointing but it is apparently very difficult to make quests interesting). Anyway, the text boxes presented where clear and consistent, apart from the reward which didn't say exactly how much it was (it just said "some gildar"). 

* Your sovereign is needed to build your first city. Pioneers are needed to build subsequent cities. But apparently no unit is needed to build improvements. This needs to be made more clear in ALL of the user interface elements throughought the game (the bad wording is already mentioned above, but this is a new angle because there is now also a restriction that you cannot build improvements outside of your kingdom's borders).

* Cities need food to grow and apparently the only way is by a farmer hero or building the farm improvement. This really needs to be mentioned as the game opens up (every time the game opens up) and since it is so important, it should even be mentioned as a warning if you build your first city outside the reach of fertile ground.

* Transfering items between units, similar as to using inventory items, is completely without interaction hints. There is no enlargement or highlight of a valid target when you hover over unit symbols dragging an item, and there is no audible or visible cue that the transfer was succesful and has been completed.

* A concrete example of why ineractions need audible and visible cues is the magical compass I just received from a quest. I clicked on it thinking I needed to equip it in order to get it to work, and it disappeared. Now, because there are no cues, I do not know if this is a bug or intended, but I hope it is a bug because I can't see you "consuming" a compass like you do with a potion or a book.

* A second example of the need for cues is that my sovereign has suddenly got 6.25 in combat rating instead of 0.25. I have no idea how this happened. Did he level up? I think his health has increased as well but I was not told if this event, nor can I in the interface available to me figure out why this change has occurred.

* A third example is when you get escort quests or quests to find huts, which then get drawn on the map. The 10-30 seconds needed to locate them on the map is completely unecessary and could easily be avoided if you gave a visible cue (but not an animated zooming sequence, that usually only confuses... just show the map and then fade in the new location with a glow to highlight it and a sound).

* Again, I received a book which promised to increase my defense, which was at 0 at the time. I right clicked to read it and it just disappeared and my defense is still at 0. No clue to wether this is a bug or intended because of... oh, you know by now.

* I've encountered another kingdom and its borders are blue. I know we greeted and such at one point, but I forgot which kingdom it was, and I see now way of finding out. The popup of the cities inside the kingdom are indistinguishable in content from a popup of a city in my own kingdom.

* I've discovered the power rating meters around the central icon when nothing is selected. It is very interesting as I believe they show the relative power distribution between kingdoms. However, I don't think my own kingdom is represented in that circle. Also, it is the smallest area yet for activation via the cursor to gain the popups...

* A further detail is that when you click the large center icon when nothing is selected, nothing happens. How about instead of requiring very precise aiming on the thin circular border, have the entire icon present a tooltip summary of all kingdom power ratings?

* In the relations screen, I am at war with another kingdom. But which one is it, and where is it? I do not find any color coded information regarding which borders I should look out for, and as mentioned earlier, I cannot see which colored borders represent which kingdom.

* In the various graphs showing historic progress, I see my own color (red) and the kingdom I'm at war with (yellow). However, on my map, I only see a blue kingdom, which isn't represented in the graph, and I've ever had our sovereign units meet in person on the map! The yellow guys (who declared war on me) I've never heard about or even seen.

* Two games in a row now, I've received encounter messages from units I do not see on the map. In this last game I might have figured out why this is. I saw an adventurer and hired him, and within his range of vision, there was a unit of different color. Still, you should not receive greetings from units inside the fog of war. If they greet you, the should automatically be uncovered by the fog.

I will edit this post as I go along...