Another way he got into trouble is that he had and still has distinct trouble with the idea of authority. Unlike Lizzie, he could never quite see that people had any right to boss him around because usually that meant that he had to give things up or act like a servant and be mistreated by cruel adults who hated happiness and fun. Point that at a lazy, gutless and entitled asshole father who overreacts to anything that pulls him into the world and away from the belief that he's owed unquestioned obedience because of white male privilege and you'll see why John had declared war of Mike's free will. About the only thing that either dolt could see eye to eye on is that Elly was out of line wanting to be more that a nanny, cook or charwoman because, as weak men, they fear strong women.
The end result of John's panicky overreaction to anything like conflict and self-serving advice (as well as Elly's being rock-fucking stupid) is the horror monster we call the Delicate Genius: a grandiose nitwit who's the inevitable end product of Mike being fucked up by his dad. While it's hard to see how he can be cured or prevented, I should think that he could have at least been blunted were Phil to have eaten John and Mike raised by someone who deserves the title of 'man.'