By 1688, both boosting the power of the crown and promoting catholicism were uphill struggles in England and Scotland, particularly the latter as there had not been an openly Catholic monarch in England in almost 130 years by that point. It would be the equivalent of a twentieth century British government trying to undo Catholic emancipation.
So you need a personality transplant, and a James smart enough to realize he can attempt either the absolutist project or the Catholic project, but not both at once. To do the absolutist project is pretty straightforward, he just continues the policies of his brother, and like his brother keeps very quiet about his religious beliefs. To push Catholicism, ironically the best move would be to agree to the Catholic exclusion act, provide there is no renunciation of the throne to his heirs. Then as Duke of York he uses his social position to try to get more of the English and Scottish elites to convert, without raising alarms about his actually becoming king. This means Mary (and not William) succeeds Charles II. If the ITTL exclusion act does not exclude future children of the excluded heir, as long as they themselves are not Catholic, it would mean that if James still has a son by Mary of Modena, that son would succeed Mary as King, with James exercising considerable influence behind the throne.
However, to do either, what is needed for James to be a Catholic and British version of Henri IV of France, or more like his brother. Even if the POD is that he has a smart advisor who he listens to, by the time he actually becomes King, after the exclusion bill controversy, its pretty much too late, though he can keep the throne until his 1701 death if he pursues a super-minimalist agenda.