First off... great game. I've really enjoyed the improvements over Elemental:War of Magic.
Alright, on with the important stuff (bugs):
Arena
Did not get my loot after completing all the battles at the Arena. I confirmed that the "blacksmith" special abilities were granted.
Workaround: None, but the stuff I got from the battles was a lot better so I'm not complaining.
Maul Attacks
The maul attack that allows a unit to attack repeatedly freezes the game during tactical battle. This includes the Cave Bear as well as any Berserker imbued weapon.
Workaround: Do not use weapons with the Berserker prefix and auto-resolve battles with cave bears. Alternatively, kill cave bears before they can attack.
Matyr enemy unit
The enemy unit named Matyr freezes the game during tactical battles when it tries to attack. This might be related to the maul attack noted above.
Workaround: Auto-resolve battles with Matyr units or kill Matyr units before they can attack.
Cannot load two games and then save
When system is low on memory (? not sure about this as I have 2 GB memory), you cannot load a second game and then try to save the game. The system will crash due to insufficient memory. I suspect a memory leak.
Workaround: Do not load a second game while in a game. Exit out of the game completely. Restart game. Select Load from Title screen.
Cannot load games that are past season 272
This might be specific to my PC but after a long game (defeated most opponents, killed the earth elemental, killed the death/swamp elemental, killed the fire elemental, etc) I am not longer able to load a saved gamed. This seems to happen after season 270 or so...
Workaround: None. Declare victory and start a new game, season 1.
Counter attack confuses game if it kills the last enemy
In a tactical battle, if the last enemy is killed with a counter attack, the game gets quasi stuck. That is, the battle does not stop. To get out of this, the user can click the "auto-resolve" button at the bottom of the screen. If the user does so, they will not get any experience for the battle (units do not level up).
Workaround: None. Take care to finish off enemies so that the last one is not killed by a counter-attack.
After defeating Elemental Bosses, the area of control is still active and prevents "construction"
After defeating the Elemental Bosses, I can't build on the "control" nodes to reclaim their lands. 1) the influence of settlements near the Elemental Lord's zone of control cannot penetrate the influence of the dead Elemental Lord. 2) my pioneers refuse to build on territory controlled by an opponent.
Workaround: None. Declare victory and take your frustrations out on the next Elemental Lord.
High initiative battles skips units/other units attack twice
In battles where units have extremely high initiatives, the combat order is buggy. 1) The list of "who is next" is not correct and jumps around. 2) some units are skipped entirely instead of going next (even though they should go next). 3) some units attack twice (in a row) bypassing other units.
Workaround: None. Enjoy your free and extra attacks on slower opponents. MWA HAHAHAHAHAHA.
And, finally, rebalance issues (that I love to exploit but make the game too easy):
Thunderstrike
AWESOME spell... especially since it only costs 12 mana to cast. End game, I literally teleport around and kill entire battalions single-handedly (especially with the help of the high initiative bug mentioned previously! twice in a row? Don't mind if I do). This spell makes Wind magic easily the best to choose from (plus stacking of initiative bonus). HUZZAH! Add in Storm and I can wipe out an entire legion of dragons with 2-3 champions. Granted, I did have a lot of wind shards.
Fixes: 1) make it cost more 2) don't bunch up the enemy at the start of battle (makes it easier to rock their world if they are close together) 3) put a cool down on the spell like other combat abilities have 4) etc. etc. etc. etc. you figure it out... I'm not paid to figure this kind of shit out.
Storm
Another great Wind spell. Did I mention you get this with Thunderstrike? This is a deadly combo. Storm hits one enemy with a lot of damage but randomly and only costs 8 mana. End game, it doesn't matter if it's a random target if I kill everything with one hit. HUZZAH! Granted, I did have a lot of wind shards though. 
Fixes: see Thunderstrike.
Teleport
Every Sovereign should know how to teleport at least for the end game balance. Otherwise, I will always select Wind magic. Cloud Walking (Teleporting) is just too important to pass up end game.
Therefore, until all Sovereigns can teleport, I will always select Wind magic or quickly find champions who already have it selected.
Blight
A spell that kills the entire world's population? Damn... Why not just give us nukes? Why would I ever cast this spell since it hurts my own people? Also... seems like it would only delay the inevitable (slow down global research and production). It doesn't solve the problem of 20 armies marching on my capital... Seems like this spell is just spiteful and a last strike weapon. Also, it takes away a spell that might have made Death magic better (or maybe equal to Wind magic, HUZZAH! the greatest magic ever invented).
Army bonuses stack?
Okay... so I thought about this and Shield-bearer isn't that bad... I mean... +9 defense for the entire army, end game, isn't that great when champions and monsters have 50+ defense. But +1 movement with the compass and other items that bless the army does stack and allows great mobility. Granted... I love this... but I don't think that was the intended intent. +11 movement gets my troop's ass in gear! I almost don't need Cloud Walking (or whatever the hell you want to call Teleport). Note that I said almost. Teleporting across the map is still pretty handy (especially at the end of the game). Speaking of which... just call it Teleport... that's what it does.