The group of six nobles and one bishop (the Immortal Seven) who sent a letter to William of Orange asking him to invade England and restore the Protestant religion, did so after the birth of James Francis Edward on 10 June 1688. The letter reached William on 30 June 1688.
Besides the support of Roman Catholics, James II had the support of Protestant dissenters because of the Declaration of Indulgence [
http://www.jacobite.ca/documents/16870404.htm ] issued in April 1687. This Declaration suspended the penal laws for not worshipping with the Church of England, allowed freedom of worship for non Anglicans, and suspended the requirement to take religious oaths before advancement to civil or military office. James issued a revised Declaration in April 1688.
In the summer of 1687, during a speaking tour to gain support for his policy of religious toleration, he said in a speech in Chester:
Suppose...there should be a law made that black men should be imprisoned, it would be unreasonable and we had as little reason to quarrel with other men for being of different [religious] opinion as for being of different complexions.
http://en.wikipedia.org/wiki/James_II_of_England#Reign .
Those Anglicans (the Nonjurors) who believed that James II was the Lord's anointed and could not be deposed also supported his right to remain king.
James could have saved his throne by forging a coalition of Nonjuror Anglicans, Dissenters and Roman Catholics on a platform of maintaining the legitimate succession and religious toleration; and if he had moderated his despotic policies. In fact, while not being a liberal ahead of his time, he could have appealed not only to advanced opinion with his policy of religious toleration, but also to many of his subjects. His argument would be on the lines that his kingdoms of England, Scotland and Ireland have suffered much from religious conflict and strife, now is the time to let each man be free to worship according to his conscience.
Part of his new "moderate" policy would be to issue writs for elections to a new House of Commons.
The idea that James II was a religious bigot and political tyrant is no longer tenable. He has been described as being either naive, perhaps even stupid, or an enlightened despot ahead of his time.
If James had kept his throne and Anne succeeds him on his death in 1701, then on her death in 1714, Princess Anne Marie d'Orleans, the Queen of Sardinia (1669-1728) would be the first in line of succession, assuming that Princess Louise dies of smallpox in 1712 as in OTL. Anne Marie was the daughter of Henrietta-Anne, the daughter of Charles I.
in May 1686 James II created the Dominion of New England. Initially this comprised the colonies of Massachusetts, Maine and New Hampshire (which then included what is now Vermont). Connecticut and Rhode Island were added in September 1686, and the Provinces of New York, East Jersey and West Jersey in May 1688.
http://www.en.wikipedia.org/wiki/Dominion_of_New_England . The Dominion was abolished in 1689.
If the Stuart succession had continued, the Domionion of New England might not have been abolished.