Just to get us started, a few things I know I need to work on:
There are instances in which either BRA or TEU convert back to Catholic after being converted to Protestant in one of the mod events. This prevents competion of the event chain to form Prussia. So maybe a check after a certain time, then autocomplete the union event with a conversion thrown in.

Also I need to make sure the player who is emperor of HRE can interact with challengers, currently they can't

You can sit and spam the decisions to get max prestige if you're large enough. I'd suggest adding modifiers that are applied when selected and go away when certain criteria are met. For example, when you select the decision and you get the modifier, the requirements would be something to the effect of "Has one of the following: doesn't own <region x>, doesn't own <region y>, etc." When this modifier is active, have the other decisions go away.

I don't mod, so I'm not certain if this works on decisions effectively. Maybe give it a shot though.

@bagel
Yea excellent point. I do need to do something about that. There are stricter rules for the AI, the human players have a lot more flexability to change decisions. The only rules I have right now is that you if you are Western Rome, for example, you can't go back and decide to form Italy. I'll look at how to make sure you can't spam prestige, or maybe put in a timer that prevents you from switching decisions for a time. The thing with the timers are though is that I think they are kind of lame. I was hoping people would just be able to enjoy the freedom to make their own decisions. I don't know what to do with this one yet.

So, I formed Rome (the western one) as Milan. A few things I've noticed:

1) The idea names and descriptions are broken
2) Every couple of months I get the "Our Brother Empire" event, there is no other rome and it seems like the text is refering to me sending myself a message... Its just giving me free 10 prestige constantly.
3) I got permanent claims as Milan on Italy when i took the decision, but since I'm no longer Milan I cant use them.

Right after teu got event that changes their religion, they converted back to catholic... maybe event should check how many provinces are protestant?

Edit:

To trigger PU both countries has to be either protestant or reformed -.- Nice

Edit:

Triggered religion change manually <.< Also ce_german_events.24.b is not localized (or I did not find it in localisation files), Im having missing localisation in this event option.

@Fabby
Thanks for reporting let me look into this for 1 and 2.
For 3 I'm not sure I understand. When you chose to form Rome you got a permanent claim on Italy and now it is gone?

@Nightliss
Hmm must have screwed something up there. Let me fix the localisation. Thanks for reporting.
Yea I actually had TEU convert back to Catholic after the event convereted them to Protestant. I've got this fixed with a new event in the upcomming patch.

Milan still has a permanent claim on Italy, but I'm Rome now, and Rome does not have claims on Italy. There are just greyed out Milanese claims all over the place now.

here is a screenshot: https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=667971672

@Fabby
Ok gotcha, thanks for the screen shot.
The latest update fixes 1 and 2. Next update I'll put in a permanent claim for Italy for ROW. You're right it makes sense.

Also, I'm still getting "Occupation of Rome" now that I've formed Rome. I think you need to update the triggered modifiers with your new Rome tags :-)

Started new game (ofc as Bra) adn it's 1453 now, Teu just got A Worthy Proposal event which apparently switched my religion to protestant, Teu switched back to catholic right after. Teu also switched to feudal monarchy but stayed Pol vassal. Somethings not right here...

Edit:

Ok 1 year later Pol released Teu and we formed allaince but still... Order is kinda ♥♥♥♥♥♥ up :(

@Nightliss
Sounds strange. You have the Protestant Reformation trigger in 1453? Yea something is up. Did you trigger anything manually?

@Fabby
I forgot about that one, yea I fix that too. Thanks for reporting

@user12343

Well the thing is the reformation did not start yet and I didn't trigger it manually. No clue why it triggrered but it did.

still getting the issue where the teutons convert back to catholic every time the event fired where they become protestant, and then they convert the center of reformation they chose to get, it doesnt make sense and is kind of infuriating