User blog comment:The Milkman/Indoctrination Theorists Say the Darndest Things, Part II/@comment-98.240.62.123-20121205063937/@comment-1440333-20121205150828

The Catalyst actually tells you  in the  description of Control that the Illusive Man could not do it as they controlled him. Ergo Shepard cannot be indoctrinated as he CAN control the Reapers.

And Saren did not want Synthesis as described by the Catalyst, he wanted organics to work with and serve the Reapers.