User blog comment:The Milkman/Indoctrination Theorists Say the Darndest Things, Part II/@comment-5830255-20121205091100/@comment-4237253-20121205153358

Indoctrination was never that important. It was a part of the story, but it was never an underlying, recurring theme. That isn't subtle at all. In fact, one of the writers of Mass Effect stated that, to him, the three major themes were unity, synthetics vs. organics, and making alliances. Indoctrination isn't that big of a deal. In your words, I'd say it's a "small side theme".