User blog comment:The Milkman/End of the Line/@comment-212.78.179.247-20120712111051/@comment-24174486-20120712183204

"Step back to Mass Effect 1: did you not kill Saren because you rejected his synthesis solution? Go to ME2/ME3: did you not kill The Illusive Man because you rejected his solution of control?"

What you're forgetting is that Saren and the Illusive Man were indoctrinated. Shepard wouldn't have much reason to believe that either option they desired was actually a possibility and would know that neither of them would ultimately carry through on either idea. Saren's tune is significantly different than the outcome of Synthesis: Saren wants to show the Reapers that organics can be useful for the Reapers. Saren was not seeking mutual peace as Synthesis results in—he would have been happy for organics to become slaves to the Reapers. On the topic of the Illusive Man, he wouldn't have been able to control the Reapers as he was already under their control, as the Catalyst points out. Allying with either Saren or the Illusive Man (post-indoctrination, whenever it was) would have essentially been allying with the Reapers, which certainly wouldn't have ended well.

Shepard's goal throughout the series has always been to destroy the Reapers because that was the only option that appeared feasible. While the Control and Synthesis choices are foreshadowed, Shepard themselves has no reason to believe either of them are possible until the ending.