"Protestant" at the time was, perhaps even more than it is today, a very broad and vague label, with the Northern princes being concerned with their religious freedom in many cases more as part of political power (In terms of the confiscation of Church property/bishoprics, administrative positions within the Empire, inheritance, ect.) and their "German Liberties" vs. the centeralizing tendencies and increase in Imperial authority being pushed via the organs of the Catholic Church. The first thing you'd need to do is create a more unified Protestant theology, where the various state churches were at least similar enough to be "In Communion" with one another in order to have a fully unified sense of religious identity. Throw in a stronger Hapsburg push to Catholize outside the Crown territories, overt favoratism towards Catholic states within the Empire, maybe have a Protestant uprising that they ask for Imperial contributions to put down...
Basically, triggering a broader and bloodier version of the 30 years war where the Protestant states feel like their continued authority/autonomy was at stake to the point the Evangelical Union gets its butt in gear, is willing to include Reformed thinking states, and puts together a united military front. Maybe as the result of Bohemia asking them to select its monarch following the previously listed series of events? Alternatively, have them offer it directly to, say, the Danish King (In his capacity as Duke of Holestein), and have him hold the title long enough for the current Emperor to die. In the following election, the secular/Protestant electors elect the Danish King as HRE, but as a Lutheran the Pope refuses to crown the "legitiment" claiment, resulting in a war of Succession that ends in the North seceding under Danish hegemony.