Solution to Aggressive Fauna
There is a solution to aggressive fish that aligns with the developers' vision. Everyone who played SN1 already knows what it is but somehow forgot.
Make the fish useful
You could kill stalkers in SN1 but that's a terrible idea for endgame reasons. Nobody complains about stalkers - even though they were aggressive fish - because they provided a unique reward for knowing how to interact with them. Similary, crash fish gave sulfur and gasopods gave gas pods. *cough* Needlers *cough*
Nobody complains about reapers or ghosts in SN1 because everybody had a fun way of interacting with them; leviathans could either be an obstacle you dodged or a trophy on your wall.
If mangos collected silver, they turn from being nuisances to jackpots. One pda entry hints that you can tame wild marrowbreaches. They're called Collector Leviathans so why aren't they collecting stuff I can steal? This is a tried and true solution from SN1.