Here is a list of things I have noticed over a few games:

• After loading from a saved game or upon exiting a city, a hero's stack movement limit is set back to 2, despite movement bonuses.  It then increases by 1 per turn until it reaches its expected value.
• Moving units out of a stack with a high movement rate sometimes gives the units that leave a temporary bonus to their movements, but only if you move all at once, not one space at a time.
• Moving into a fight loops the movement sound and animation in the background until you click OK on the battle summary window.
• Here is one for some debate:  Should traits that give bonuses to the unit's army stack, or just use the highest bonus?  It may depend on the trait.
• The Ledger screen does not show production, so you can't use it to find a good city to build stuff in.
• Once you queue up a building to build, you can't tell what it does.  Maybe make the tooltip for the build queue show what the building does.
• There is no indication in the unit icons down the left of the screen as to which units have moves left.  WoM had this.  Where did it go?
• Technologies that have prerequisites in another field are not indicated very well.  Prerequisites within the field are indicated by connecting lines.  Could you add some sort of extra lines to indicate cross-field prerequisite techs or techs that allow techs in other fields?
• Being able to queue up more than one tech for research would be nice.
• The Drake's death animation and sound effects are out of synch.  The sound takes much longer than the animation
• It takes a while after casting Heal for the next unit to move.  The animation trails off a bit long.
• Casting shrink on a mounted hero (I noticed on two Empire heroes, not on Wargs) makes the unit really tiny, like Chihuahua sized.  Funny, but a bit extreme.