The Back Story states that the various Ancient machines were created for the benefit of those who couldn't use magic, yet most of them can be operated only by people with Shadows (i.e., magic-users).
Perhaps it's a kind of failsafe to prevent them being abused or used as weapons?
So Kluke wants to be a doctor, and her parents were doctors. Why isn't she a White Mage? She's a Black Mage, which should be Jiro, who is a White Mage.
Their Shadows responded to what they wanted to do immediately after eating the light spheres. In this case, Jiro wanted to heal the injured Kluke, and Kluke wanted to have the ability to fight alongside her male friends. I think that's the official explanation given in the game, but they do gloss over it a bit.