We are talking Novels. I don't believe Zhann had given people a deep look into her past in novels. (Books without pictures.)
Vader was threatened by Xizor. So, Mara Jade could very well have been a threat. Xizor and Mara both had the Emporer's attention, and Vader could very well feel threatened by this. If I remember right, Vader tried to kill of Xizor on many ocassions.
Vader = Human/Machine
Mara = Human
When it comes to the Expanded Universe, I would bet that the Emporer saw more potential in Mara than Vader.
What would be a nice twist to EU is that she does kill Luke. There were hints to her perceptions in the last Mara & Luke novel. Mara still seeps back to the days of the Empire.
R.I.P. to 'The Source' and 'MacCorp'