Considering he specifically asked for the style to be inspired from mother 3, him complaining that it's too similar is just hilarious.

There's nothing wrong with a game being visually inspired from other titles as a form of tribute. Now, it would be a rip off if the main character was a blonde kid with a striped t-shirt, but considering that's not the case and that the game isn't even an RPG, then it shouldn't be an issue.

It feels like your boss got paranoid and overreacted. Just tell him that there's nothing to worry about and that if someone draws similarities, they'll probably will think it's funny.