Sure..
THe Pantheon idea seems easy yet flexible.
3 good, 6 neutral, 3 evil
3 of the neutral would be played by computers and would be the sea nations trying to overrun the lands. (this might be seen as evil.. I know
but they will be a separate team none the less)
In the course of time you could have the 3 player controlled neutral nations choose sides for either good or evil. (maybe not a real choice but create an event in their nation that would make it look like one of the other sides was really insulting them (though they'd probably be at war anyway .. but I'm sure something can be thought of) so they'd join the other side.
Then in the progress of the game you could have some lands turn to sea (change map) to help the computer races a bit and make it look like the water races are conquering the lands. If you give computer controlled waternations a boost and don't give player races that can easily acces the water they might put up a decent fight.
In the end good or bad would win... and then maybe be forced to fight eachother.. or something. Or let a final deathmatch decide which god will rule the Pantheon.
Not terribly original but it would work
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