The main barrier to a stronger Bavaria unifying Germany would have to be religion. A Bavarian-based Emperor would be the symbol of Catholicism in Germany, and it would be difficult to see the Protestant states of the Empire voluntarily uniting under a Catholic house that was the dynastic successors of the Hapsburgs that had fought so hard to extinguish Protestantism. So in some ways even a powerful Bavaria might fall short of uniting Germany, possibly having to content itself with Southern Germany, and leaving the North to some confederation under Prussia or one of the remaining Protestant States.
Is this really insurmountable? Prussia ruled over Catholics in OTL, after all.