It has been a long time since I read the works of Frank Herbert and his son, nevertheless, it appears to me that Duncan was brought back repeatedly with the ultimate goal of making him the "Kwisatz Haderach".

This is born out in the "final" novel authored by his son and co-writer culminating with the syntheses of Duncan's mind to the machine, Erasmus, in order to bring peace between man and A.I. and to rule them benevolently.

It seems to me that the Duncan thread that runs through the stories is the purely human link (as others suggest) that Herbert sought to retain, to preserve as a kind of hope for all humanity, that we might learn from the past and make a better future for mankind instead of one devoted to self destruction. Duncan, I believe, was Herbert's hero in that he represented qualities of devotion, loyalty, duty, honor, as well as a kind self reliance, independence, an uncompromising inner core, and an unfailing desire to make oneself better.