Dr. Robert Child and the Remonstrants:
Here is the famous remonstrance by Dr. Robert Child et al., in a tract published by his brother John in London, with additional documents. The following text is taken from Tracts and other papers relating principally to the origin, settlement, and progress of the colonies in North America from the discovery of the country to the year 1776. Collected by Peter Force. Vol. 4.
Child and the other petitioners asked for toleration of non-Congregational puritans (Presbytherian, here) and Anglicans, for their admission as Freemen, so they could vote and get elected, and for a reanglicization of the colony. So what was at stake was the survival of the New England Way, the control of the electorate and of civil office by the Congregationalists, and more generally the growing autonomy from England, as Massachusetts was perceived by some as considering themselves a free state.
I haven't managed to find the "counter-remonstrance" written as a response by Dudley and Winthrop, but hints can be found in the relevand passages of Winthrop's Journal (from May 1646 to the end of 1647).
Projet AlbionŠ 2000-2002