I like arkham's suggestions, and I'd like to add some input.
1. Religion. I second this notion. One cause of tension between the colonies and their motherlands (and other colonies) was religion. The Catholic French and Spanish and the Protestant English/British and Dutch led to the Seven Years' War, the founding of St. Augustine, and other conflicts in Europe and the New World.
2. Rebellion and Loyalty: I like this, too. Remember that not all of Britain's colonies rebelled in the New World. Florida remained loyal, as did Canada. With Spain, not all of its colonies rebelled at once. It first lost New Spain in 1821 and its South American colonies all rebelled later, and even then, it held on to the Spanish West Indies until 1898, when they were lost to the United States.
3. Other Nations: I agree with arkham entirely. If it weren't for France, there would not be a USA today. In Colonization, you can't seem to interact with the kings of other nations, even after you see them appear in the New World.
4. Lack of Supplies: I'm not sure how I feel about this one. Maybe if it were that units can't heal unless there's a supply train with them, then that would work better, like in the Charlemagne mod for CIV.
5. Diplomacy: Again, not sure how I feel about this. Diplomacy was not really an option for the Spanish or the English colonists when fighting their wars of independence with regards to their mother countries. However, diplomacy with other European nations might work, but that falls back under the "Other Nations" category.