It would be huge. Bavaria as a unitary, modern, staunchly Catholic state was probably the decisive factor for the outbreak of the 30 years' War and the early victories of the Catholic side. Austria would not have been able to pull it off alone. With Bavaria Lutheran, even if it was only the lukewarm, nonmilitant variety so common in Germany at the timew, the earlky seventeenth century would see Austria in a much less favourable position,. Quite possibly there would be no militant Counterreformation, and thus no Bohemian Revolt. If there were, it might well succeed. Bavaria would be a threat to Austria as a potential "protector" of its Lutheran minorities esp. in Upper Austria and Bohemia.
Also, with Bavaria going Lutheran, the chance of Catholicism holding out in the Rhineland diminishes seriously. Bavaria would have limited interest in the imperial status quo (there will certainly not be any talk of an electoral dignity or control of an electorate spiritual). It might decide to deliberately upset the applecart.
No Swedish intervention, most likely. Continuing greater Danish and Dutch influence in Northern Germany. Perhaps Sweden focuses more on Poland and the Baltic (or they don't go abroad killing people, maybe). North and Central Germany would look very different.
No Westphalian settlement. The HRE might fragment, either tearing along confessional lines or, IMO more likely with a return to sanity in Vienna, shedding its northern periphery.
Protestant Bavaria would make a huge difference.