In another Rpg game I played we where supposed to be controlling an empire. A few where decided by the GM to be "main opponents" and played every action every turns and got every income, other where decided neutrals. That means that played like every 3 turns and got only the income for this particular turn. They were supposed to be catering to internal problems during the other turns (to make micromanagement easier).
Transfered to Dominions, this would mean that every independant nation would be considered a player, but played only every few turns, and got their income only when they played (when they do not play, they get income 0). When they feel strong enough, they could go attack their neighbours. That would also means that every few turns independant would get bigger and bigger, and get better and better spells and research. Since they "play" we also could include a possibility to "buy" the "country" instead of conquering it by force (but only if they believe in you as a restriction ?) or giving funds to them (in case you want to have a indy as border with some of your neighbours.
It's probably too big a modification to be included in Dominions though...
This is a bit different from the subject but I'd like it if indy magicians got better and better as time went by.