User blog comment:The Milkman/Indoctrination Theorists Say the Darndest Things, Part II/@comment-98.240.62.123-20121205055835/@comment-24174486-20121205124710

You may want to consider that Shepard opposing the Illusive Man not necessarily because of what they want to do but how they seek to achieve it, and also the little fact that he's indoctrinated.

Also, if you'd paid attention to the narrative, you'd realize that there's nothing stopping Shepard from going against the "themes" of the series in their choices. Choosing Destroy arguably goes against the Paragon way of thinking—you're utterly destroying the enemy while throwing away allies.