Honestly, the Reformation as a whole feels fishy. It is not only something that pops up quite a bit early, but also tends to spread like crazy pretty fast and thus in turn leads to a rather early Protestant League war compared to real life history..
The historical 30 years war was from 1618 to 1648, but I generally see it happening it anywhere from 1550 to 1580-ish. Not just that, the counter-Reformation as a whole is kinda pathetic, actually resisting and reversing the reformation is basically something that doesn't happen normally without player intervention. Unless dumb luck/misfortune leads to the reformation centres being in say, the British Isles as a whole.. I generally see most of Europe under Reformation in short order...
For example, I am currently doing a Palatinate run, normal and everything. Allied Austria, gathered land etc.. mostly ignored the entire religious conflict since I thought it wouldn't matter since it's Austria's problem and I would just convert to whatever is most succesful down the line if necessary. Then suddenly I become emperor in around 1560 to 70-ish and check, yeah Austria is under PU with Spain so I am suddenly emperor and have no clue what to do. I have never been emperor before and given I was so late in the game I had no idea what to do or whether I should even try to "fix" the HRE or just abuse my position to get more land safely.... and then like a month later or so the League starts popping up and filling with members...
Only a year or so later later and the league war starts and I suddenly have to fight half of Europe.. fortunately I have Spain and Poland and England on my side, so they help me a good deal etc.... I win the war and get religious Supremacy...
Then a few years later I drop it because I am getting gangbanged on all sides by the damned Centres of Reformation. Two are in one nation, so forcing Religion only got rid of that one. One is allied to blobby Burgundy and I couldn't fight it evenly without help from my allies who are all in debt. One is my PU Ingoldstadt who I cannot make get rid of it.. I try to resist for a while but am unable to do anything as my provinces get converted faster than I can even convert them back.. not to mention as time goes back the remaining provinces have zeal so I cannot touch them... then I get excommunicated due to some random event and say screw it and convert to Protestantism...
You would think that decisively crushing the Protestant League would actually damage the faith's ability to spread all over the damn place. But nope, just a few years after the war the Emperor Palatin, 4th Great power with PU over Ingoldstadt, Landshut and Bohemia drops his crown and the Empire crowns Cyprus as the next Emperor. (They are currently beating up the Mamluks for land.) Wonder how that would be explained in the history books...
Right now, huge chunks of Europe are Reformed or Protestant even though the Reformation experienced a crashing defeat in teh HRE war...
image link here.
Moreover it would be quite common for rulers to have a say in the religious policies of their vassals and even allies. It would also make sense for the player to be able to force religious concessions on the Pope via warfare or papal control.
Historically, a lot of nations didn't convert because the population enforced it. If I remember right, Sweden's leadership converted and it got enforced on the people.. I think there should be a influence of alliance and rivalry. The Emperor's allies should have higher resistance to Reformation, or at least a better ability to fight it back than say the allies of the first nations who swap to protestant/reformed...