Biggest difference being that Morgause will do whatever it takes to get where she feels things should be, while as you said below, Merlin will only do 'bad' things when he has no other choice.

I'd like to see more of Merlin make his own choices like he did when he let the dragon go free. You know, choices that he makes without having the dragon's voice howling at the back of his head. Like you said it might make him weary of Morgause giving him advice... but I'd like it to be honest advice.

With her having known Igraine, I think she wants him gone for personal reasons, not just to usher in Arthur. I mean, Uther is responsible for Igraine's death, and it's understandable that Morgause would harbor hatred for him because of that.

I certainly think it is these personal reasons that drive Morgause. I think it's one of the reasons she was so annoyed when having revealed the truth to Arthur it didn't end with Uther getting what he deserves. I can't help but notice that in trying to get both Arthur and Morgana's trust, she did so in trying to turn them/fan their distrust of Uther. Morgause's own hatred of Uther I think is perfectly understandable and I'd like to see it explored further. She has so many reasons why she would want him dead.