You questioned Shade's origin, I merely answered.
You're concern about the gym leader kids do not make sense to me. The story doesn't revolve around them, in fact you freed them and battled them later. Like it or not the questioning of their absence in the gym can be summed to "Who cares?" Well, I know people do care such as yourself but it's not going to benefit you anyway in knowing. You still got to battle them and claim their badges.
Regarding the orphanage, I actually just recall that they still can battle for their badges it's just that Radomus doesn't allow it. The first time you met him, he considered but decided against it. Even though you are a trainer he used legal actions to prevent such battles. That much was explained and it makes perfect sense to me.