UB Is overpowered. Moves fast, does high dps and can self heal + stun. Whats missing? He has no drawback...
None of the Assassins really have drawbacks, though.
Rook's HP too high? UB dishing out too much damage? I don't intend to stop it. If a Rook wants to specc tank, let him pump points into HP. If a UB wants to specc damage man, let him pump points into weapon damage. But what points? Attribute Points.
I propose a second skill tree. Well, I guess it wouldn't really be a tree, but all upgrades have been laid out in that fashion (skill and citadel). Basically, it would be an Attribute Tree. The format which I have devised this is a direct rip from the current upgrade path mechanic. I believe that it could work better, but I'm keeping with what we have.
Anyway, without further adieu, allow me to present... MS Paint on a Touchpad!!!

That is the essence of what I propose. Each level, you get 2 Attribute Points that you can spend on any Attributes with an available level up. Level requirements for Attributes would be 1-10 and 15 just like skills. Different levels would cost different amounts of points.
Levels 1-2: 1 Point
Levels 3-4: 2 Points
Levels 5-6: 3 Points
Levels 7-8: 4 Points
Levels 9-10: 5 Points
Level 15: 6 Points
This basically prevents people from spamming everything worthwhile to max level. With this system, you would get 40 total points in a game. Maxing out a skill would cost 21 Points. This is a drastic change from the current system. You could only really fully upgrade one attribute line. You wanted Demigods to have multiple roles? Strengths and weaknesses? You can pick your poison.
So what would you get for fully upgrading a line? For most Demigods, I would have to say a greater effect than if it was currently lv20. It could be coming earlier, yes, but it would also be coming at a much higher cost. They wouldn't be lv20. They might be doing lv20 damage, but they would have awful health and no manna at all. They might be able to tank through everything, but they wouldn't be able to cast many spells or hit very hard. (This system would allow the Rook to keep his huge 8k HP... if he fully upgraded it.)
But this system can really take a turn for Generals. In short: Unit Upgrades. I propose that, in addition to the General's ability to upgrade his/her own stats that they should be able to upgrade Minion stats. I think Generals should get 3 Points per level in order to help manage this, as all the upgrades would come from the same point pool. If you wanted to make an Assassin-General, then you could compensate for his lower stats by pumping all your Attribute Points into your character. If you wanted an unstoppable army, you could boost your minion health and damage...but don't forget to upgrade your own HP!
The current Morale/Enhanced Stats (or whatever it is called) would basically turn into a free Attribute level. If you selected this on the skill screen, you would simply gain however many Attribute Points you would normally gain on a level up (2 for Assassins, 3 for Generals).
That's it. Its really that simple. Unfortunately, I kind of lack some important knowledge. What stats are actually increased when you level up? I'm assuming HP/Regen, Manna/Regen, and Damage/Atk. Speed are all increased (at least, I'm fairly sure about Atk. Speed). What else is upgraded? What else could we include for upgrading? Armor? Movement speed? I currently balanced it assuming that HP/Regen, Manna/Regen, and Damage/Atk. Speed are the only things upgraded. If other things are upgraded and/or could be upgraded, then things should definitely become cheaper.
Of course, everything is hypothetical. Don't tell me its a stupid idea because my numbers are off. Tell me what numbers you would use instead. This is just a rough outline.