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Just Hungry is a site about food. There are 
bonito flakes vs. fresh fish
Eric, the main difference between bonito flakes and fresh fish may be the fact that bonito is dried and concentrated - sort of the way dried mushrooms taste quite different from fresh. But in many coastal areas they would make soup and stuff without the bonito flakes, putting fish in instead. You can use konbu seaweed + fish bones, heads, etc if you want to make a pretty rich fish stock. It won’t be the same but should be very tasty. (also a lot more work!)
Some time ago I made a fish quenelle soup, which is similar to fish-ball soups you can get in Japan especially in fishing areas. That kind of soup is usually made with a simple kombu dashi.
Hope that helps!