The Europeans reported the three sisters methodwith some tribes in the northeast. The accounts are all very jumbled and contradictory. The tribes in New England also appear to have have been relatively new to growing. All three species were not found together in New England before the 1300's. If they did grow them this way they could only do it one season in a location. They would have to change locations then next year.

Fundementally you can't plant corn/pumpkins repeatedly without a break. It's a mega attractant to the rootworm beetles which are endemic to North America. If they did not rotate they would have crop failures after only one season. Beans also have all sorts fungal and bacterial diseases. The only way they could control them is via rotation/fallowing.

What was done in mesoamerica for thousands of years was rotation. They were the ones that domesticated the three species and built large civilizations from the extra food availability. They grew bush and vine beans, corn, and pumpkins. They also grew casava, tomatoes, peppers and other species. When yields started to decline, they would fallow the ground and move their plots.

There is evidence that the Mayans for over 500 years mostly figured out how to avoid fallowing their fields. They would grow 3 cycles per year in rotation for a large surplus of food.