I don't agree with that, that's the problem. I want it to stay paused until I explicitly unpause it, as was the behavior in all previous versions.
Ah, see, in CK2 it always seemed to work like if a notification paused the window, clicking it away would unpause, so I got into a habit of quickly pausing again after dismissing windows, or at least checking to see if I was still paused. Maybe I'm wrong about that, but that's my muscle memory, at least.
I don't disagree with your logic that a game when paused should explicitly wait for the player, I am saying that I feel as though I'm used to it already so it's unnoticeable to me.
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