This (starting a faction) sounds more like expansion material to me. But it would definitely be cool. Especially if they were fully autonomous and you could kind of be the 'don' of your group. Say you were a world renowned alchemist, so much so that you banded together a group of others with similar talents and started your own guild. You could micromanage their activities somewhat, but if one of your members was making money selling potions of a lesser quality than you wanted you would have to dismiss him or correct his ways or kill him.
Like I said this sounds like a lot more work than is needed for the base game, and it wouldnt appeal to everyone so it wouldnt be worth shipping on disc.
About the mini game activities, they would be a welcome addition to me. From things like smelting metals and forging weapons a la Fable, to hunting quests and challenges like Red Dead.