We, are the Time Lords, we'll always save the day!
Well, they come from space. They're the last good members of their species, in this case the evil ones are the Master and the Y.D.G. Also, they can reform after death, able to stay the same or turn different. Being rocks, the Gems possibly have very low-body temperature.
They're both magic aliens too. Also, they both fight alien organizations. So, is it a stretch to say: "Maybe they thought it would be nice to have the son of the Doctor enter fantasy?"