Ever wonder just how Bowser. Jr. and the Koopalings are related? In an interview with Nintendo Life, Nintendo's Akira Otani is asked that very question. While the answer might not be as detailed as we would hope, at least we get some kind of info.
As far as the Mario & Luigi series goes, it really is in Paper Jam that the Koopalings became more featured. The character setting for Koopalings is that they aren’t Bowser’s children, they just work for him! That’s the same for Bowser Jr.’s Journey, but the Koopalings have to take care of Bowser Jr. because he’s the boss’ kid.