I've found that some of the metals and crystals can be useful later (you can use crystal samples to get the microscope pictures, and you need crystals for the JA relics). I've perfected every harvestable, so I keep a couple of those on hand. I don't keep fish, except for the expensive ones that can be used for fertiliser, and I've never managed to get all the bugs from OR.
What annoys me is that I have complete collections in the treasure chest or around the house, but the collections tab continually forgets that I've got them all in my legacy save.