umm.. you obviously didn't read the books well enough to understand the reasoning behind the storyline...
i've read them all twice at least (except for Heretics)... The Duncans were prized military commanders and Leto just liked having him around. I think he also had Duncan cloned so many times just to spite the tleilaxu and show them that no matter how hard they tried to make a ghola that could kill him, he would always withstand the attack.
Also, Leto chose to transform himself into the sandtroutish thing in order to preserve humanity. It was the way he had to go to prolonge the survival of the human race; it was the first step along his "Golden Path". In short: if he didn't do it, humanity would have been destroyed.