I think the main problem with Morgana is that the actress playing her isn't very good at being a villain. She's got better, but when she first turned evil a couple of series back it was really noticeable how unconvincing she was.
If she was better at playing a villain then this wouldn't be a problem. A well written bad guy with a real talent for acting evil can quite easily come back again and again and never lose their charm. In some cases they can even become more interesting than the protagonist.