Sorry Mike1988, but I think your explanation is inaccurate. I think it would be better to say that the use of the past perfect is often optional in the spoken language (as in the informal written language and, increasingly, even in the formal written language. However, there are some situations where it has to be used to avoid ambiguity. Also, of your three examples, the first and the third should be in the present perfect, while the second, without any further context, should probably be in the past simple.

It is rarely used in common spoken language. It indicates that action had alreayd done in the past. He had written this novel and now it is read by almost every child. I had spoken with him long time ago. She had mastered many languages and now she do not want to continue her studies.