There are so many information, and details for the internal factors, however, I believe that the biggest difference they show among the three societies (Northern, Middle, and Southern) would be external because the geography and the environment is totally different. For example, for New England, the climate was very cold, which resulted in having less mosquitoes (no diseases such as malaria, or yellow fever). Not only that, but the economy was based on trade since the soil wasn’t rich to grow abundant crops, due to cold weather. Lastly, this colony had a war with the Pequots, which resulted in the Pequot War (which was the bloodiest war in colonial history).
Moving on, for the Southern colony, Virginia, the climate was very warm. Due to that, there was long growing season, however because they had settled in the swampy area (James River), there were many mosquitoes, as well as not-fresh water. Because of this, vector-borne diseases, fecal-oral diseases were common. As mentioned before, because of the fertile soil, the economy was based on cash crops (a.k.a. tobacco). Additionally, they had conflicts with the Powhatans which led to bloody slaughter, annihilate due to religion, and racism, and burnt down houses as well as crops.
Lastly, the middle colony had a moderate climate, and mixed economy which was based both on trade as well as agriculture. Not only that, but unlike the other colonies, they had peaceful relationships with the Native Americans. Overall, these different facts of geography, and environment had changed, and defined the difference between the North, Middle, and the Southern Colony of America.