The Plymouth colony was not set up by the same Puritan group that later started the colonization of Massachusetts Bay Colony. It was set up by the Pilgrim Fathers who were from a more extreme "Separatist" Puritan/Calvinist sect, who had earlier taken refuge in Netherlands.
The Plymouth Colony existed separately from Massachussetts for about 70 years. What if it had been granted its own separate charter after the the dissolution of the Dominion of New England.
This would keep OTL's southeastern Mass, an area somewhat bigger than Rhode Island and containing Cape Cod, its own entity. How would this continued territorial separation affect the 18th and 19th century.
A parallel What if could be made about Maine, what if it had remained separate from Massachusetts?
Finally, given all the other colonial timelines around here lately (WI Jamestown failed) what about a different alternative, what if the Popham colony of 1607-1608 in Maine survived?