Hm, maybe less Brandenburger particpation in all those wars against France at the Rhine? That would be bad for the HRE, even when the armies were still small and even before Frederick Williams reform, the Brandenburger armies were quite high quality since the time of the Great Elector... as for the efefcts on the eastern territories getting more attention, Im unsure. I would say the Hohenzollerns already very aptly developed them as is, so Im not sure there is still much further potential to grow...
Yes but the effect hit a lot earlier than the great elector, Brandenburg inherited the territories in 1614, while the Brandenburgian army to say it mildly was quite pathetic and the Junkers was growing in power. Which gave the Hohenzollern a incentiment to focus on their new Rhineland territories, which was economical richer and under threat from Catholism (and as such more likely to support increasing princely power). Beside that without focusing on the west and potential intermarried with the Calvinist princes there, I could see Johann Sigismund not converting to Calvinism. If we look at the Protestant League most of the members of it was either South German states, or they was Calvinist, Brandenburg, Anhalt and Hessen-Kassel was the only North German state to join the League. It's quite likely that a Brandenburg here stay out of the League, which mean that they can succed in embracing nautrality in the early 30YW. Whether that's enough to butterfly the Danish phrase of the war away, I'm not sure off, but the fact that most of the North German states are staying out of the fighting or as in Saxonys case joining the Emperor, may keep North Germany so quite, that Christian IV of Denmark can't convince the Lower Saxon Circle to join the war.
Of course in OTL, the Swedish semi-occupartion of Brandenburg allowed Elector Georg Wilhelm to extent his power over the Junkers, in effect he used the Swedish occupation to remove their freedom from taxation through. The dissolving of the diet was later push through against the Elector reestablish the Junker freedoom from taxation again. Without that we see the Junkers stay much stronger, and they may in time extend their power over their estates to the same degree, the knights of Mecklenburg did. Of course without Swedish intervention into North Germany, Brandenburg inherite the entire Pommern rather than only Hinterpommern (based on the Treaty of Grimnitz).
So we see the Great Elector dealing with a state, where the Junkers are stronger, but also one which aren't depopulated, and where he has control over the entire Pommern and have dominance over the Oder, but lack Magdeburg, Mark, Cleve and Ravensberg (on of my map spell it Ravensburg*). The situation would demand different policies.
*And it's a translation of a German book, where it's spelled correct in all the other maps.