I agree that it's a hard and interesting problem. Yet other countries seem to be managing it better, or there is something structurally different.

I read somewhere that one of the key issues in Germany is that freight and passenger trains share the same network. While a delay of 15 minutes can be wildly problematic for a passenger train (missing connections, stranding at some godforsaken train station etc.), it is virtually irrelevant for freight. Then again, that should make it easy enough to always prioritize passengers over freight, but either that isn't being done or it's still insufficient.