Stories are about characters facing challenges and crises. They're about what happens when things go wrong, and characters tend to suffer because it raises the stakes of the story. It's not that the writers hate any of their characters; it's just what drama demands. If everyone were happy and safe and fulfilled, there'd be no story.
In this case, though, the reason the Ancients fare so badly in Atlantis
is because they're so powerful. If they were alive and well and active, they could solve the big problems themselves and there'd be nothing for our heroes to do. They have to be taken out of the picture so the Atlantis crew has to carry the responsibility for saving the day.