Geez...so many inconsistencies and things that have already been dealt with...
#1 - First off Shepard isn't indoctrinated. He is the process of being indoctrinated. The reason the breath scene supports IT is that it is the only choice in which Shepard lives, doesn't give up (throwing gun away), doesn't get the "indoctrinated eyes" (eyes of saren and TIM both of who have been leaders that were indoctrinated and are advocates for Control / Synthesis).
http://t3.gstatic.co...r0D9tcsUng08-8wDestroy is also the only choice (pre-EC) that didn't benefit the Reapers in some way. Control lets the Reapers live and rule over the galaxy. Synthesis is just accomplishing what the Reapers goals were from the beginning.
#2 - The Prothean Vi's can only detect those who are already INDOCTRINATED. Not people who are undergoing indoctrination.
#3 -In ME3 Shepard becomes the very icon of the resistance of the Reapers. To have him as a Reaper puppet would demoralize the entire resistance and make the war go much easier for the Reapers.
To kill him would accomplish the same effect. Either way to the Reapers it is a win win. Some how Shepard always makes it out. So as a back up for failing to kill him the Reapers use indoctrination (their most powerful weapon).
4- Once again...Shepard isn't indoctrinated. Reapers can only control him if he is indoctrinated. Why he is the focus? As I said in #3 he is the very face of the resistance.
#5 - Project X...I agree...not enough to go on.
#6 - Once again with the most popular inconsistency. Shepard isn't indoctrinated yet. He is undergoing the process of indoctrination.

Your Conclusion - From reading your blog it is certain you haven't fully realized what the IT is stating. Also on the fact of "having been based on just one pinnacle scene and dozens of speculative context and content, is merely a fan based opinion and should be moved into the fan portion of the forums" is complete BS. There are many on many pages of proof and hints placed by BioWare that lead to the fact that Shepard is undergoing indoctrination. I would recommend politely for you to analyse what you are arguing against like any proper debater before you decide to make such claims. It just makes you look foolish otherwise.