Just adding to the list after last nights gaming session, a few notes I made on bugs/ tweaks:
Throwing knife not working (seen this mentioned a bit)
Special weapons you pick up don't always list the stats in the preview until after they are equipped
Popups can overlap and cascade badly (ie having research window open, battle initiating, perks being given, city leveling all trying to open up at once)
Icons on popups retaining the sword or speech bubble icon
All sounds but ambient cutting off after awhile (may have come from switching from one monitor to another too often)
Auto explore - sometimes doesn't seem to initiate properly/at all (no explanation given why it doesn't). Once has a really hard time ending my turn because of a scout on auto explore not using its movement, and the turn refusing to end until I had manually moved the scout.
One sound used - I think its for construction completion, but also if you click on a place to send an army if its already on route - quite loud and sounds almost static-y?
Quest bug - Slaver quest that didn't complete after deciding to kill the slavers rather than offer to let the main unit join (I did try going back to the initial site several times)
Quest bug - rampaging umberdroth - the umberdroth never seemed to spawn, so I walked around with my salt porks, never able to figure out how to get them anyplace. Couldn't turn them in at the quest start point.
Stun trait - is this working? I used it on a drake, the popup said it was stunned, but it received its next turn and attacked on it. I don't know if the problem is that the enemy was unstunnable, so the popup of stunned was incorrect, or if its the trait. Or maybe the unit just had insane numbers of attacks.
Gamblers (luck?) trait - also unsure if this is working, the base attack always seems stronger than using the skill, at least with a bow.
Champion death in battles - not sure if its a bug or not, but if a champion dies, but the army wins, there is no penalty given to the fallen champion (negative stat). This might be one of the reasons that champions seem OP. Always giving penalties whenever they fall might slow down champion growth.
Auto advancing camera focus on next unit on main world map shouldn't occur when a battle is starting with the previous army.
Berserker axe (seen it mentioned other places) - with my 30 dex champion, did 12 mauls in a row on a deadly beastie. Said beast never dodged, it just died after getting 200+ damage in one attack.
More preferences /thoughts:
Perhaps the popup screens can fill more of the main screen (champion screen, etc). Would help legibility at high resolutions. Its not bad to the point of unreadability, but thought it would be nice.
Tactical combat camera - its okay, but I like to zoom in sometimes to see my characters, then I have the camera snap around a lot when it heads over to my archers. Again, okay but a bit annoying.
Tactical AI - one thing it doesn't do is kill off the weak - at least on standard difficulty. At least smarter enemies I'd like to see chase after that unit with 2/80 HP I moved 2 squares back from the front line if they can catch it and wipe it out, rather than switch over to something with 60/65. Likewise, basic MMO style targeting priorities (get the healer, the glass cannon DPS, then worry about tanks, etc) might be nice someday. At least for smart baddies.
World AI - didn't do all that good of picking up things. Had a Capitar NPC that built a city in the middle of a wildland (shroud?), was doing fine defending it, but never picked up any of the shaman tents or cobwebbed ruins. It could be that the AI didn't have many champions, but I got some very good things from walking about, so tasking the ruler to get them would have helped them a lot.
World AI - probably should focus more on outposts than cities, and have that mechanic strengthened to make outposts favorable to city spam. Ended up with a ton of captured cities, and the AI building a lot of cities to get just one shard or building cities in cramped areas that the city couldn't expand in anyways (between mountain and ocean with trees around.
Not any real showstoppers there or anything that majorly bugged me, but my thoughts as I played (ahem tested!) along.