Hopefully you haven't downloaded it yet, as I had to real quick push out a version 16.1, due to bugs in the merchants. Should all be fixed now.
I agree that the inquisitor should only stick to their own nation, to avoid some inquisitor from across the map turning up and upsetting your dark empire. Wouldn't make much sense, since they wouldn't have any legal authority, and could lead to very tedious work for the player, checking every nation every turn to make sure they aren't getting an inquisitor.
Localised situations (threats and victories) are reasonable, I agree. I think it's at least somewhat done, with the dark empire being at least free of concerns about evidence or inquisitors. The climate change should also be handled, since it reduces parts of the map to just snow, which you can then ignore forever. Possibly it does need a bit more balancing, to make this a bit more reliable. We'll need to look more at the end-game, now that the core mechanics are in, and enough agents are implemented to give a good variety of options to the player in the beginning and mid-game. Ideally push towards some giant final battle between good and evil, where the player can bring their stuff all together, and the NPCs can try to form some kind of last stand against you.