So I realized recently that my villain isn't very deep and is in need of some serious development...

Mortious: Power-hungry, he developed a long-term scheme to gain control over the throne. He manipulated the king's brother-in-law, Oberon, and arranged for the assassination of the king. Oberon became reagent due to Mortious' behind-the-scenes working, and Mortious has been quietly taking his enemies off the scene ever since.
He fears that the true heir, the prince, is actually alive, to the point of paranoia.
He's hired a large number of mercenaries that are loyal to him alone.
He views Oberon as his puppet and would not keep him around except that he needs someone on the throne that he can control... for now.
He has a low view of women, thus he underestimated the importance of the princess, the only known living member of the royal family. Now that she is older, she has made herself a threat.

Does he enjoy being a villain, or does he wish he was better? Does he believe he can keep the power in his hands? What do the people think of Mortious' puppet-king? Does he fear the people at all?

Has your experiences with the princess changed your view of women? Do you have a plan in case you find the prince definitely alive? What do you want, other than power, more than anything in the world?

Why is he power-hungry? Was he pushed around as a child, or maybe even completely ignored? What will he do once his puppet has served his purpose, will he take the throne himself? Is there anyone he admires? What's his favorite color?

I'd say he enjoys it, at least he doesn't feel any desire to be a better person. He's a tad on the maniacal side...
He's not stupid, he knows that power is fickle, but it just means he fights to keep it and it begins to add to his paranoia.
The general public would not even know Mortious' name. One would have to be very involved in the politics of the kingdom to really understand what Mortious is doing.
He sees the people as a whole, so individually they mean nothing to him, but he knows that the lower classes can turn violent if pushed too far too quickly. His version of oppression is subtle.

"The princess is... an exception. It was a mistake to ignore her... she has developed an inconvenient set of morals and the idea that she has... influence she can wield to counter me. But she will be dealt with.
"Of course I have a plan. And I have had twenty years to fine tune it.
"To be feared."

He likes control, specifically over other people. He felt controlled when he was growing up, controlled and belittled. It began as bitterness and became a worldview.
Well to take the throne himself would either require becoming related to the royal family or staging a complete coup, so for the time being he's biding his time. He's convinced that the prince will reveal himself at some point, and isn't willing to play his full hand until that happens. If he were to take over, he would not leave any competition alive, including Oberon.
His admiration is more like competition. The ones he "admires" are the ones he wants to outdo. Some of these are from history, others he knew in his lifetime, but he wouldn't leave them alive. He sees himself as paying them a compliment by deeming them worthy to be his rivals.
He likes purple, as it represents royalty and luxury to him, but he surrounds himself with black and red because he knows that people associate those colors with evil, so they are a part of his manipulation.

What is his ultimate motive? (A desire for power is not a good enough answer. Find a deep, compelling reason for his desire.)

What would you say were the defining moments in his life that brought him to this point?

* goes psychiatrist * So, Mortious... how do you feel?

How does he react to any hint that might come along that the prince is still alive, since he's paranoid about that? Does he ever come close to revealing too much of his power and too many of his secrets in an effort to deal with the possibility?

Is he optimistic or pessimistic?

Who did he love most when he was a child?

Did he have a father? What was his relationship to his father?