The HRE was weakening during this period, definitely. I've always found it odd how there's an inexorable strengthening of the HRE over this period in EUIV, rather than a devolution of its power over time, as happened historically.
In a way, I wish there were three major tracks to take the HRE down:
1) Religiously intolerant, diplomatically or forcibly bringing heretics back to the fold, becoming internally more centralized under the Emperor amongst adherents. -- This is the state of the HRE pre-Augsburg.
2) Religiously biased, trying to keep Catholicism dominant, but allowing Protestant/Reformed to exist within member states, or shedding intolerant unrepentant princes that wanted full religious freedom. -- This is the state of the HRE post-Augsburg.
3) Religiously tolerant, showing no favoritism at the state level, keeping its borders and member states, yet becoming increasingly decentralized, all at the cost of alienating the Pope and those nations (Protestant or Catholic) who wanted to be raving zealots. -- It would be an "alternate" history choice if you adopted this early in the 16th Century. This is ideally/arguably the state of the HRE post-Westphalia, though there was still much bitterness and distrust, and more the de facto case post-Enlightenment.
These major courses of steering the HRE were the actual choice Emperors were faced with historically. The failure of the Edict of Worms, and the Peaces of Augsburg and Westphalia showed that, over time, it was harder and harder for any Emperor to unilaterally enforce his views on the Empire as a whole. So the question is: how do we keep the Empire together when it is religiously heterodox?
It also raises the entire question of the HRE itself. After all the Schmalkaldic League was an alternative to the HRE proposed by the Protestant princes of the 16th Century. It also admitted reformed Denmark to its ranks.
I would hope a Thirty Years War scenario might allow for the formation of more than just a temporary coalition. The Schmalkaldic League should be a formable confederate state of Protestant/Reformed nations, with a lot of the same rules as the HRE* with Electors, etc. -- but for Protestant/Reformed nations. Member states needed to contribute forces -- historically, 10,000 infantry and 2,000 cavalry -- for a standing army. It existed from 1531 - 1555. It only devolved back into its separate states which resumed infeudation under the HRE because of guarantees they were given by the Peace of Augsburg.
The Confederation of the Rhine (1806-1813), and the German Confederation (1815-1848) further show there were alternate desires to form a united "Germany" apart from, or if Austria had gotten its way under Metternich, as an extension to, the HRE.
Right now, again, color me underwhelmed at this representation of the Thirty Years War. I remain hopeful in the long run to see Paradox truly give meaning and depth to the entire Reformation/Counter-Reformation/Enlightenment evolution of Europe.
But... this dev diary was not what I was looking for.
* Generally, I also believe there needs to be ways to have more "Empire"-like structures in the game than just the HRE. Confederations like the Hansa or the Schmalkaldic League, even player-defined delineation of separate territories inside large sprawling blobs, etc.