Lets discuss here why Madara wiped out the clan he created and why he left Itachi and Sasuke alive.
My theory for Madara teaming up with Itachi is that he couldn't wipe out the Uchiha clan by himself. It seems that Madara is in a weakened state and hence needed Itachi's support.
It is clear now why Sasuke is kept alive. Itachi needs his brother's eyes to get the ultimate sharingan. Still I believe that Madara needs Itachi and Sasuke for something bigger. Does he need the brothers to strengthen his own powers. If so, how? By having one of them gain the ultimate sharingan and in turn transplant the eyes to his own body? Or will he gain control in a Orochimaru's way by transferring his own soul to the new body? Or he could kill the new ultimate sharingan user and instruct Pain to control the body using the Rinnegan?
And why would Madara wipe out his own clan? Does he want to prevent that other ultimate sharingan users are born and hence he will lose the secret of the ultimate sharingan that only he knows? Is he afraid of new powerful oppositions making his life tougher? And of course, he is now the only one with eyes to control the Kyuubi, for sure he wants to keep it that way.
So everyone, what do you think?