A "flexible" variation I remember was the idea of Pantheon. Nicely RPG but the end-game was to have a 4-god pantheon such as fire, air, water, earth. Or heaven, earth, hell, fairie. Or god of war, love, fertility and death.
I think it was set teams from beginning to end but if you did it in the normal open-ended style then switching sides can take the form of stealing away their god of war to be our god of death.
