In 1648, Prussia was still the electorate of Brandenburg-Prussia. Brandenburg being the region around today's Berlin, historic Prussia being a stretch of land just west of today's Gdansk. Although German, Brabdenburg-Prussia was no part of the Holy Roman empire and in fact, never would be. Although it would by 1815 have inherited some smaller counties in the western part of Germany, about 70% of its territory lay east of Berlin.
Scenario 1): Historic Prussia -the stretch of land between Stettin and Gdansk- and not Berlin takes the lead in Prussia-Brandenburg and the state is focused on Poland, Lithonia and Russia then on 'Germany'. After the Napoleonic wars, they show no interest in uniting the German states, leaving the job to the Austrians. Eventually they will be either swallowed up by Poland, pressed into joining the new great-German commonwealth or split between the two.
2) Unification starts as a kind of European Economic Union of the states of the Holy Roman Empire. Eventually -like the EU- they morph from a strictly economical union to a political federacy. As Prussia was never part of the HRE, and mostly way out east for most of the smaller German states, it is never invited in. Not being part of the HRE, most states view it as not part of the German world, much like they would view the Swiss.