Kind of a long post, so I bolded the titles for each sub section to make reading the bits you're personally interested in a little easier; also here is a table of contents listing the headings for the truly TL;DR diehards amongst you. 
---
Power of Monsters / Getting Hemmed In (Already Set to be Fixed)
Pacing of the Game - Turn SPAM AHOY!
That's a City? Looks Like a Blob to Me. (aka, So. Many. Gardens/Houses.)
Quests. (So a Nobleman, a Knight and a Wolf walk into a bar..)
Level Up! I AM MOAR POWERFU- Oh Wait. False Alarm. Not Really. :/
Closing..
---
Power of Monsters / Getting Hemmed In (Already Set to be Fixed)
In my first game, I didn't completely agree with cmarcel about the high level mobs all over the place causing the game to be unfun; I had a lucky enough start location where I did in fact have a few things I was capable of fighting around, and I had fairly free movement of the map, only a few bottlenecks created by mobs too dangerous to go anywhere near. Then.. In subsequent games, I never had this luck again. In my third game for instance, I was hemmed in completely, north by mountain range, south by enemy AI, east by some swamp creatures (one of which was OK, but the leader was insane) and to the west by mountain range, and, through the only valley passageway I did have, by trolls.
Needless to say, I wasn't really going anywhere that game. Now, Brad has already mentioned this is nonintentional and that Beta2 was almost delayed so that they could fix this. So I'm not too worried about this in the long term. I would suggest perhaps having a low chance (5-10% range) of something somewhere spawning outside existing power levels that you just have to avoid though!
Pacing of the Game - Turn SPAM AHOY!
This was particularly bad in the game I mentioned where I wasn't able to move my units a lot. Turns consisted of setting a build queue for my city (I didn't even have room to set down a second feasable city!) and then turn spamming. There was nothing else to do.
Yes, with the mobs balanced out, you can move around more and have more to do, right? Well... Sort of. Even in my first game where I was really very lucky with positioning and got to explore a goodly portion of the map, there was STILL a great deal of turn spamming.. Set my Sov to go somewhere, set any exploring heroes I had to go somewhere, make sure build queue had something in it, then... ready.. set... CLICKCLICKCLICKCLICK.
Is anyone else experiencing this? Am I, "Doin' it Wrong"? Very curious to hear others thoughts on this.
That's a City? Looks Like a Blob to Me. (aka, So. Many. Gardens/Houses.)
As excited as I was by the city build process as presented on paper -- and heck, even by video 
-- I've become less of a fan after getting to try it out for myself in practice.
Mostly that's due to the pita that is house/garden juggling at the moment. Particularly if you luck out of having a fertile ground near you. I think that Gardens and Houses should either have their base capacity increased, or the requirements put upon them reduced.
Although to be further specific, the first level or so of city building is actually not that cumbersome. Everything after is though; unless you're willing to build a slum (no thanks ). Now, I get that there should be some trade off here. There IS an easy option of the slum presented, I get that. But while the hut to house upgrade almost doubles capacity, the upgrades beyond that are quite minimal, I believe there is on the order of about a 12ish difference between house and villa? (Not in game presently to double check it, but it was 1x difference I'm sure).
The other issue I have with cities is aesthetic.. And I'm not totally convinced there could be anything done about it at this point. They do seem to be to just be a blob, a sprawl of really quite random tiles all hunked up against each other with no roads or anything. This is is probably outside the scope of fixing now, but it also isn't really a deal breaker by any stretch.
Quests. (So a Nobleman, a Knight and a Wolf walk into a bar..)
Can has more variety? It's been mentioned to death already, but escort quests seem to be flavour of the day.. All day every day all over the place. I've also seen the Knight quest a few times each game, and the Wolf one at least once (which is freakin fantastic when can actually get to it, but again I must sadly question if it isn't a little TOO powerful).
I'm sure more quest variety is forthcoming however, so will leave it at that. 
Level Up! I AM MOAR POWERFU- Oh Wait. False Alarm. Not Really. :/
Levelling up at the moment is really really underwhelming. Don't get me wrong, I'm not advocating some power curve so steep that a level 4 will always wipe the floor with a level 1 regardless of anything else. But currently the curve is so shallow as to almost not bother. Sure, I guess by level 20 or so you would see really quite a significant difference over where you started.. But anyone want to put a wager on a Lev 20 sov vs a Lev 1-3 Sov that has done the wolf quest?
As it stands, you gain SIGNIFICANTLY more power from books/potions/items that you find about the place than you do levelling up. Level means essentially nothing. It's not useful for guiding your decision on relative power at all.
Suggestion? (Although it's just one of several possible solutions)
Make it so that where items are concerned, they cannot increase your stats by more than 50% of base. For instance, if you have 10 hp and find a ring of fortitude, it'll buff you to 15 hp, but will scale with your level and that base value increases. (Up to a maximum of 20hp or whatever the item has).
Exception to this rule being if your base value is <2. If base value is under two, it can bring you up to 2. But it won't go beyond that point until your base value warrants it. i.e., if your base value becomes 2, the item can then buff you by 50% of that, for a total of 3. For example, you have 0 attack power, and find a sword with a max of +5 attack, it can bring you up to 2 attack. If through potions or levelling, you raise your attack power to 2, this same sword would now grant you +1 over this (50% of 2) for a new total of 3 attack.
Where potions/books/other permanent stat raising items are concerned.. Just make them far, far rarer in my opinion. In the first game I played where my hero could move about quite a bit and I got several cities up, I'd encountered quite a large number of these stat increasing objects. I think 2-3 maximum over that gamespan would have been a better figure.
Then, for levelling up itself, to make it more exciting and rewarding feeling? In addition to the points allocated to the player to spend, apply a retroactive +5-20% bonus to current stats. I would suggest about 10% bonus. Apply it to the base stats, the derived stats can look after themselves as a result.
Also perhaps reduce the granularity over the stat control (at least on the level up interface, you can keep that level of detail in the background) and perhaps if necessary reduce the number of points allocated to spend. i.e., Instead of having 10 pts at level up that increase a stat by .1, maybe give 3-5 points but have them actually increase a stat by a whole 1.0 or at least a 0.5.
These sorts of changes would all, I think, make levelling up feel more like an achievement.
Closing..
That's all I have for the moment. I was going to talk to resources a bit as well (such as the plentitude of 'Materials' while everything else was a struggle (relatively))... But then I played a game where I focused more on creating units, and was like, 'Ah..' so I don't feel quite so confident talking to that point yet. May bring it up later!
I have to be honest and say the issues I raised so far have detracted from the enjoyment of the game. The pacing and mob problems in particular.
They have. No two ways about it. Not ready to throw in the towel by any means though, I still have high hopes for the project. And heck, even if I detest the base game.. With the mod tools available..! 
If you read this far, thanks! Feel free to leave some thoughts.
