User blog comment:The Milkman/Indoctrination Theorists Say the Darndest Things/@comment-4220180-20121024022116/@comment-24174486-20121026052131

It's not just in how it's established in the ending but how everything prior to it supports it being their goal. We're given nothing to indicate that Shepard is indoctrinated, and a very strong piece of evidence against indoctrination—the Prothean VI Vendetta, who is established to be capable of detected indoctrinated beings and does not find Shepard to be indoctrinated. It's also in how the Reapers throughout ME3 do everything in their power to prevent Shepard from reaching the Crucible, whereas in MS the Reapers want Shepard to reach the Crucible—effectively going from "kill Shepard" one second and "preserve Shepard" the next.