Sounds like a good idea, however, at the core of it all is your sovereign; what would he do? I don't like playing the bad guy. I'm more of a grey area type of character with a preference to use a small evil to achieve a greater good. Because I am predisposed to good I should choose a faction that belongs to the kingdoms, since they embody fairness and justice, but the reaity of it is that it only paints half the picture of who my sovereign really is. The Empire has death magic and respects the rule of the strong and awhile this isn't his style I feel as though the empire holds the key to the quickest path towards power which suits my soverigns true ambitions perfectly. When he finally conqueres the world, he will usher in an age of prosperity at the cost of so many smaller evils and injustices. Lore says the channler lives hundreds of years longer than a normal human so whats a few decades of strife compared to centuries of peace? When he takes over the world, he will cast the empires views aside in favor of a kinder approach, and the last evil thing he'll do is probably purge the people he feels are wicked from his empire.

^Long explanation.

Short explanation ( for those of you who don't like to read. Why are you on a forum any way?)

My overall point is this. I like your idea but since this is as much an RPG as is an RTS your sovereigns character should factor into the picture. Since my sovereign is only using the empires outlook to further his own personal goals, he isn't incapable of mercy, and therefore wouldn't enslave the refugees. Options should be given based on the all possible playstyles and to accomidate the role playing aspect completely.

I think I understand your point. As far as being consistent goes I'm going to assume you're worried about factions becoming too undefined with the introduction grey areas - and I agree that it shouldn't happen. Limiting these grey areas would be important to preserve the working idea that are the two powers in the game, but as a big RPG fan, leaving grey areas into the mix appropriately has never diminished a game I've played. What comes to mind when I think of this is Neverwinter Nights.

To me it only makes sense to let the player decide to do with specific resource nodes like that.

Below this point has little to do with the OP'S suggestion. I'm merely explaining the effects of a evil minded sovereign joining a kingdom faction, creating a grey area for evil players as suggested.

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As far as a personality operating opposite of my sovereign I'd have to say the results could be quite interesting. To give you a good answer I'm going to have to make assumptions about good and evil and the nature of the sovereign. This is how my idea relates to the way I envision this game.

My first assumption pertains to the idea of a sovereign.

Since any sovereign is in control of a faction we can assume that their ultimate goal is power.

Now for an assumption about Good and Evil relating to power.

The quickest path to power would be one that ignores moral obstacles and obligations. A good person would take the longer route out of moral obligations to ensure justice and fairness, while an evil person would take the quickest.

The next assumption I'm making is about the grey area in between good and evil relating to both my sovereign and your sovereign.

My sovereigns intentions are to gain power in the quickest way possible so as to transform the world into a more positive force. To achieve this power, he would then side with the empire, and dismantle them later when they were no longer needed. Now, since your sovereigns goal is power just the same as mine, yours would logically calculate that the empire is also the fastest way for him to achieve personal power and so he would never waste his time with the kingdoms system of government.

It could be argued that infiltrating and dismantling the kingdoms would be the fastest way to bring about their destruction, however, we have to take into account that you are simply a faction with an idealogy and that you are represented as such in every game. When you start a game, there are kingdom factions, as well as empire factions and then there is you. You do not represent the kingdoms absolutely.

That being stated; if power is our ultimate goal as is suggested by the game itself, then an ultimately evil minded leader would never cripple himself or his route to power by founding or leading a faction with the opposite idealogy - however if he were leader whose obligations were ultimately good, he would have no problem using an evil idealogy to further his ascention, if it were quicker.

It gets more complicated if we assume your sovereign doesn't understand his role in the world and has chosen kingdom and realizes he's evil. 

Just as you can use evil to do a greater good, you can use good to do a greater evil - but then that would be evil for evils sake, and doesn't affect obtaining power, which I've assumed is what the games about since it is an RTS/RPG.

 Like I said, these are assumptions I've made about the game itself and what the devs are attempting to do with the whole RPG element.

Let me know if it makes any sense. I couldn't think of a shorter way to explain it.