I once had a weird idea start that what is now Netherland or parts of it take over Germany in some unified group, or a form of 'Low German' 'empire'...
There is a third Habsburg heir to Charles V - he gets the Netherlands. As the Reformation takes hold, the Niederland Habsburg line converts to Protestantism, and the Kingdom of Niederland becomes the dominant power in northern Germany, acquiring Cleves, Julich, Berg, Mark, Ravensberg, Munster, Westphalia, Liege, Treves, Cologne, and Paderborn. And Ostfriesland, Oldenburg, and Bremen.
The Counter-Reformation gets even nastier, being a family quarrel. Niederland leads a Protestant coalition to a decisive victory over the Catholic Hapsburgs, and the King becomes ruler of Bohemia, Moravia, and Silesia. The Imperial title ends up with the Protestant Wittelsbachs, who get Bavaria and Austria.
Turks sack Vienna, and Hungary becomes a Turkish vassal kingdom under the Protestant House of Rakoczi (not very far from OTL).
Catholicism is wiped out north of the Alps.
Eventually there is a Revolutionary/Napoleonic convulsion, and the HRE is consolidated into 20 or 30 states. Niederland is the largest. When push comes to shove during final unification, Niederland has much better leadership than the Wittelsbachs.
Prussia, incidentally, ends up as an independent German-speaking state. There's another in Tyrol-Styria-Carinthia-Carniola.