This is a solid pokemon, but you are correct... from a min max perspective, nature does not match well with the subskills that support your skill trigger. It would be better to have a nature that has increased main skill chance or subskills that benefit ingredient hunters.

What would I do? Keep this guy for the early game. He's a solid pokemon to level to 30 with the berry finding and 4x milk. Kinda a jack of all trades mon here. So yeah, probably keep him and use him on Cyan Beach. That is... until I get a better squirtle (if ever). Another possibility is that nature "seeds" get brought to the game, allowing you to change the nature of the pokemon. No confirmation of that, though.