dharper's article about his system of Religious Leagues in HRE from there: https://forum.paradoxplaza.com/forum/index.php?threads/m-t-1-22-dev-diary-8-religious-leagues.899088/
Although it's not tested as well as I'd like, I've finished a revised League War system for the Holy Roman Empire after the Reformation begins. It's a bit different from the system in place now, so here's a quick walkthrough.
The event chain begins with the Diet of Speyer - or the equivalent, anyway. This will fire as early as five years into the Reformation, when at least a fifth of the Empire belongs to a heretic religion. The Emperor then has the choice of which religion to make dominant in the Empire, or whether to tolerate them all, with obvious effects on the princes of the empire. A few years later, the Diet will be recalled and the Emperor can confirm his earlier decision or reverse it (as can other, later Emperors). This can be a way for the Emperor to avoid a League War - but usually, a League forms in protest of the Emperor.
When the League forms, you get the possibility of a League War, with either the Emperor or the League leader beginning it. Unlike vanilla, this war doesn't have the peace option of enforcing your religion on the empire. Instead, whenever the war ends every member state of the empire gets to cast one or more votes to decide what the empire's state religion will be, with a simple majority needed. In other words, to win you need to force-convert, annex or vassalize member states, especially the electors with their extra votes.
However, this kind of victory may be short-lived: if at least a fifth of the empire remains heretic, then they may form another League later on. After the first League War, any country can join the leagues, and countries may be asked to send support to one side or the other - especially when the side they support is losing. That's an effort to prolong the wars, although it's only been moderately successful - I still haven't seen anything close to the Thirty Years War in test games.
One improvement that players may appreciate is that now the Emperor can force the League War to start by declaring war - or, if neither side begins a League War, an event may fire after 20 years which can force a war, or result in a peaceful conclusion by holding another Diet. With each Diet (and each new war), member states become increasingly willing to accept compromise. Once the Empire accepts religious tolerance, no more leagues will emerge (with the exception of the early years of the Reformation) - but that doesn't mean it's impossible to enforce religious unity, just hard.
There are almost certainly still bugs to catch and iron out, but I think it will be less frustrating and more transparent to players this way.