Mr. Gogeta34 wrote...
Could argue that since they want Shepard unaltered:
Harbinger: "Preserve Shepard's body if possible"
They probably are intentionally not indoctrinating him and want to study him when this is all over.
That's my view, but not completely.
During the "wave" fights at Object Rho, Harbinger's voice clearly says "Your mind will be ours," or something like that. So I do think they'd like to indoctrinate Shep. What they don't want is the short, intensive kind of indoctrination that turns people into nervous maniacs. The powerful form that leaves them capable, like the form used on Saren and Benezia, takes time.
Even Kenson had the willpower to resist indoctrination long enough to build a facility on an asteriod and rig up the engines. If she'd been fully indoctrinated long enough, she would have dismantled, sabotaged or otherwise incapacitied "The Project" just to be safe. It would have been as simple as corrupting the VI guidence so the asteriod would miss the Alpha Relay, for instance.
Shep's exposure simply hasn't been long and sustained enough. He/she spent two days at Object Rho. He/she spent, at most, hours on the dead Reaper and was never inside Sovereign.
As for the Prothean Beacon theory, it did provide Shep with a vivid vision of what the Reapers really were. Remember that Saren saw the beacon's warning only after he was fully indoctrinated. Seeing what the Reapers really are before indoctrination begins to take hold can't make indoctrination any easier.
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