I do not like the idea of having civs bound on allegiances. Maybe they should tend to some allegiances, but not being permanently bound to them. Saruman and Sauron should be able to go to war with each other, Gondor could fall as easily as Númenor, the Dwarves could ally with the Easterlings to raze the Elves.
Also, it has another inconvenient: balance. Power would change drastically in a game with randomly selected civs - imagine if you played Gondor only to discover that all the AI civs were all allied. Or if you selected random, and all of a sudden discovered yourself a permanent vassal of an AI civ. Or how weak should one of these vassals be should they end "alone". On a scenario, this might be fair, but not on a mod intended to be played on a random map.
Making all civs independent allready gives you a chance of defeating some "forces of evil" without defeating The Shadow. It's only that these forces need not be the same every time...