Provisos:-  I haven't read all the feedback provided here, so may repeat what's already been said.  I also haven't finished a game, and my experience of the different factions is fairly limited.  That having been said....

Stability

1.  As some others experience (and has been reported elsewhere), alt-tabbing still causes a "DX Error: Invalid Call" every single time I try to do it.  I've suffered this in every version to date. 

2. Sometimes the screen will just go black and I'll get the message "Elemental has stopped responding".

3. Sometimes on exciting the game I get the message "Elemental War of Magic has stopped working".

GUI / Graphics

1. Mouse pointer "persistence".  Often as not I will have the wrong mouse pointer for the screen I am on.  This most often occurs when I level up as a result of combat.  The mouse pointer stays as the "move here" pointer you have on the tactical combat screen.  Similarly if I am aiming to initiate combat with a mob and click on it on the same turn that I finish research the mouse pointer on the research screen remains "crossed swords".

2. If I start a new game without exiting the game I often lose detail on the cloth map.  Not minor detail - mountain ranges etc.  Typically also they'll be some awkwardness around how my cities are displayed.

3. Magic research - on completion of research some times I'll be prompted and my spellbook will open, sometimes I won't be.  I would prefer it if I was always prompted.  And if I was always prompted the additional indicator in the top right hand corner of the screen would be unnecessary.

4. Character sheets can be opened and closed by clicking on the portrait.  The equipment screen can be opened by clicking on the little icon at the bottom of the protrait, but it can't be closed by clicking on this.  It would be more intuitive if it could be.  Likewise clicking on the city build / training icons opens the repective screens, it would be good if you could close them in the same way.

5. I've noticed that, sometimes, perhaps dependent on the zoom, when you click to construct a building, placement can jump to somewhere you didn't expect.

Gameplay

1. Sometimes wandering heroes can be a little arbitrary in their nature.  In one game, when I had twenty odd heroes, every single one of them was an "adventurer".  This strikes me as a little extreme.

2. Is the New Pariden start subject to the same "location process" as other starts?  The reason I ask is that on a few occasions the bonus starting city that the New Pariden faction gets is extremely poorly located, with no special resources (including fertile land) within a ten square radius. 

3. Inability to exploit metal and old forest resources.  I might have missed something in the release notes but I have never been able to build a mine in beta 4.  There doesn't seem to be any indication why either which leads on to my next point.

4. There seems to be a general lack of feedback on the constraints in play on city development.  For instance I had one city, next to an area of fertile land, that had a workshop, a study, arcane research and a merchant.  I could not build a farm, and I could not build a hut.  They were simply greyed out with no additional information (in contrast, in most starting locations like that have no trouble building the farm and the hut too and getting underway properly....).

5. Quest markers could be clearer.  Sometimes they only appear the turn after you would expect to see them (witchy hut thing with the key).  I had one occasion when the next piece of the forge was in an utterly unreachable location (bar lowering land or building a ship - and I couldn't build the ship because I didn't have any metal, in spite of having cities next to ore locations).

6. Strategic spells - those that effect cities.  I've not been able to get them to work (this might just be me being a twit, but even so some feedback would be useful).

7. Newly recruited heroes - they never move until the second time you've ordered them to move.

8. Offensive spells in the tactical screen feel, to me, a little arbitrary.  There is huge variability in the damage they put out, from 0 to 11 say, with no predictability.  As a result it's hard to work out which spell should be more or less effective against which type of mob.  As a result pretty much the only offensive spell I cast, when I get it, is Chain Lightening.

9. Lastly, and amusingly, the random name generator can come up with some very odd names for worlds and towns.  Some of them verging on the "nsfw".