You could argue, that the Electoral shifted from one branch (the Palatinate) to the other branch (Bavaria) of the house of Wittelsbach. Also it wasn't just the Electoral Rights, Bavaria also gained the Upper Palatinate (north of Lower Bavaria). Bavaria kept the Electorate and Upper Palatinate, the Palatinate getting a new electorate as compensation was more like a compromise. The Catholic side kept Bavaria as an Elector, though the Protestant Electors were fully aware, that though the rulers of Bavaria and Austria shared the same religion, on worldly matters they were often rivals.
Also Saxon Electorate shifted from the Ernestine to the Albertine line of the house of Wettin; here the Catholic Charles V worked together with the Protestant Maurice of Saxony (in fact the coalition made by Charles included Catholics, but also some Protestants princes) against John Frederick of Saxony and other Protestant princes. One branch lost it and the territory connected with it in favour of the other, but it stayed with the same dynasty.
As for a new electorate, creating it for another house to reward them is one thing, but the emperor creating a new one for his own house, that may not go down all too well. If the Emperor were to control the territory of an electorate and or have a dynastic claim over one, which results in a conflict, then maybe a new electorate (a la the Palatinate) could be done, IMHO creating a new one as a reward (a la Hanover) for yourself, would be harder to sell to the Prince-Electors and the Imperial Diet.
Alright then.
But I'm still curious about the effects of the Reformation in Hungary. Their queen is one of the Habsburgs "more" open to the "new" ideas, but Catholic Austria and Venice are right next door, while Muslim Ottomans are going to be expecting tribute or else...
Also, from what I've read, Louis seems to have been rather rash/immature. Was this perhaps simply because he WAS young, and given time, could/would he grow up? Or would it result in Marie having to take charge of government because he's too busy playing Joffrey Lannister-Baratheon?