The early period of the Middle Colonies would have to be considered the 17th Century. The Middle Colonies were considered a part of the British Empire during this period. The government system of the Middle Colonies reflected this imperial relationship. In each of the Middle Colonies, a royal or proprietary governor was appointed to oversee the government and economy of the colony. The governor had to be tactful and pragmatic as he had an especially difficult balancing act. To be successful, he needed to keep two competing factions happy: the colonists and the royal government in England that he served. On several occasions, the governor was dismissed at the behest of the throne and at other times by the colonists.
In addition to a royal governor, the Middle Colonies also had elected legislative assemblies. The assemblies made laws and oversaw taxation policies. The relationships and degree of authority between the governor and assemblies varied widely depending upon which specific colony you are examining.
The Middle Colonies, in the early period, all enjoyed the rights of religious freedom and did not pay taxes if they did not have representation.