Okay, this may get a lot of brimstone,
What is Shepard isn't indoctrinated, but his surroundings are? Shepard, at this point, is at least 50% mechanical, which can be controlled externally?
Shep's eyes most likely didn't survive space in the beginning of ME2, so organic/synthetic replacements had to be made. Bones, muscles and nerves had to be rebuilt, using partial tech.
This makes Shep already partly synthetic, which is a step ahead of the Reapers. The Reapers can't take over in their usual manner because Shep has already upgraded to their level of tech invasion. So, they use a massive pulse from Harbinger as he's approaching in London, and rewrites a massive portion of the visual/tactile processing software.
Since the Reapers would be using memory from onboard hardware, they would use what Shepard had seen before (eg child, Normandy taking off unharmed, dead/dying soldiers). But...they would alter what is actually present.
This way, Marauder Shields could be an Alliance soldier trying to go through with Shepard; the Reapers don't want independent eyes inside, so they make the soldier look like a Marauder, which causes Shep to open fire. Same for the Husks.
Finally, the Reapers *own* TIM, and use Anderson either as a foil, or a visual/audio overlay of a husk or something to maintain the illusion. Admiral Hackett is then either faked, or allowed to transmit, getting Shep to try doing more.
Enter Casper the Kidly Ghost. Leader of Reapers. Slayer of Thumbless Masters. Killer of Gamer Hope.