Okay, let's begin. That promised post on Francois II. Okay, first question--is the healthier Francois II Charles IX healthy or Henri III healthy? If the former, he'll probably live longer, but there's always the danger of a sudden turn of bad health carrying him away--if the latter, he'll probably get a decently long reign. So, let's go with the second. It'll at least make Mary's marriage happier. Stick in a butterfly net, so that history goes about the same, right down to daddy's horrible fluke jousting accident--and now we begin.
Now let's start with something simple--the Guises are going to be movers and shakers in Francois II reign, especially the start. However, at this point in time that is not instant Huguenot-persecution--Cardinal de Lorraine is the unofficial head of the family in politics and he fancies himself a Catholic reformer. Lorraine thinks he can get everyone onboard with his great big religious compromise wherein the Gallican Church becomes more Huguenot-friendly, and the Huguenots respond by becoming more Church-friendly. The problem is he can't--his plans may be popular with the French elite but the rank and file reject them, the Pope doesn't like them and there always enough firebrands and opportunists on both sides to stir things up. However fond his wife is of her uncle, Francois is probably going to get tired of the Cardinal promising peace and not delivering--Lorraine probably resigns from the government.
At this point, French government is going to be dominated by the same problems that it faced OTL--toleration is unpopular, but persecution is untenable. To the good, the Guises are likely not signing up with the Catholic radicals--but that might actually make them harder to deal with, as now they don't have leaders with a commitment to things not going entirely insane. Still, with a long-living, fairly healthy king with a male Catholic heir things should probably go all right in the long run, provided he doesn't end on the wrong end of someone's knife/shot, always a possibility.
Now whether the union with Scotland holds is another matter. Mary is probably going to continue to try to push for mutual toleration between Catholics and Protestants, which will comfort some and alarm others. At least two very important people are probably going to want this union dead, one of whom should be no surprise--Queen Elizabeth of England--and one who may very well be--King Philip of Spain. Both of them will have misgivings about supporting a movement to depose a seated monarch, but both of them are also pragmatists about things like this, and neither want France to be able to threaten England from Scotland. (Indeed, England and Spain probably stay on better terms ITTL.) Of course, this doesn't mean that any such attempt will succeed, but... well, life in Scotland is going to get interesting. (And, assuming something starts up in the Netherlands, France is likely to meddle in that--enjoy the cross-confessional plotting!)
So, those are some of my general ideas on the matter. My apologies for not being more specific, but so much depends on so many variables--does Francois, Duke of Guise get killed, and do the Guises become convinced that Gaspard de Coligny is behind the killing?--as to make it very hard to see exactly how it will turn out.