I mourn what could've been Mal's relationship with Simon and River in later seasons tbh. You could see that they were really taking their time to flesh out and build that mentor/paternal relationship between him and the youngest crew members throughout season 1. They never rushed it. Which is something I feel that a lot of shows struggle with nowadays. The pacing was perfect. You could see Mal go from reluctant saviour of the two strays, to actually seeing them both as part of the family crew by the end of season 1. You can see him become more fatherly towards River (like when he takes the gun away from her saying "Honey, you want nothing to do with that" or the last episode when he gently tells her that there is a place for her on the ship and takes her back). This makes sense, as River already expressed that she viewed Mal as a sort of father figure (not so subtly, in the witch episode, she says that "Dad" was going to save her and Simon).
Simon on the other hand, having taken over the caretaker role for River, is not as emotionally open and can challenge authority if he feels something endangers River, which I think directly clashes with Mal because the latter obviously needs to maintain order on the ship for the good of the entire crew. Not only that, but I think Simon did not deal with the pain of being essentially abandoned to his fate by his own father, which he might be unwittingly projecting to his next authority figure, Mal.
I think the series was building up to a big moment between Mal and Simon, where perhaps Mal finally broke down those barriers that Simon set up and showed him that, unlike his father, he would never abandon him or River to their fate, that he would always be there for them. That Simon is not just there because he's useful as a doctor for the crew but because they all want him there, because Mal wants him there. And perhaps this would allow Simon to finally allow himself to be more of a kid, and let someone look after him for a change and accept Mal as his new father figure, as someone he can trust and depend on.
