The indoctrination theory is what got me into MEU but it just seems a bit over speculated & analyzed. What makes Shepard so important that Harbinger must indoctrinate him? If TIM was really under the reapers control why order him to bring back Shepard? If we are really indoctrinated why doesn't harbinger just assume control of us? In project overlord David did that to us so why not Harbinger?
Shepard has done the impossible. The first organic, and now half synthetic to have forced the Reapers plans back. Shepard is a symbol of hope for the galaxy's future, since as the story progress Shepard can bring the galaxy together. Not to mention Shepard inspires others to follow him/her into what ever situation he/she may face. Having Shepard on the Reapers side is a huge insult to the galaxy. Sure killing Shepard would bring hurt to everyone, but Shepard would become a symbol for all, that he/she gave all to stop the Reapers, where as the Indoctrinated Shepard brings everyone's moral down, for if the galaxy's greatest hero can become indoctrinated, then everyone is doomed.
It depends. Many of us believe TIM wasn't under full Reaper control until the end of ME2. He had Reaper implants in him long ago, but were never activated so to speak. Much like a sleeper agent, and a back up plan if anything happens. With the collectors destroyed, Cerberus becomes the Reapers new black ops team. Overall I don't believe the Reapers had any intent of bringing Shepard back, and that was just Cerberus/TIM doing what is right. However in the end TIM becomes the Reapers slave at the end of ME2.
We are not indoctrinated yet, we are undergoing indoctrination. If Harbinger pushed/forced Shepard to become Indoctrinated, Shepard would result into a mindless husk, like the Salerians back on Virmire. they want Shepard intact. Tis true Shepard can die, however the body can still be of use. That and it's a win win for the Reapers. Shepard is dead, or is converted, both benefit the Reapers, only an indoctrinated Shepard is a far more win scenario for them.