Have you ever been at a speech or meeting and heard the following response from a question: "That's a great question," followed by the answer to asked question.
What's the point in this little preface? Why bother complimenting the question? Is it just filler?
I think it is mostly used to buy the person answering the question some time, but there might be some other psychology behind the scenes. Maybe it is used to hide a bad answer. If you say something nice about some one, they might be more likely to accept a mediocre answer.
I think it's a bit wasteful. There really is no purpose to commenting on the question by saying it's a "great one." If it's misleading or loaded, sure, you can make a comment. You could even preface it by saying something about how you might not have the expertise to full answer a question. But saying "that's a great question" doesn't add anything.
The next time some one begins answering one of your questions with "Wow, that's a great question," do every one a favor: interrupt them with "Thanks. I expect a great answer in return."