So let me see if I understand all this correctly.
- Shepard has proven remarkably resilient against indoctrination. (Debatable. If you didn't play Arrival, Shepard hasn't spent more than a few hours in the presence of Reaper artifacts. Even if you did play Arrival, it took months to indoctrinate Kenson, not days...)
- The Reapers conclude that they need a special will-breaking hallucinatory form of indoctrination to break Shepard before the ordinary form of indoctrination will work. (Speculation, but hey, it might be true.)
- The ending of ME3, from Harbinger's blast onwards, is this 'special' indoctrination. (Also speculation, though this section does have a fair amount of 'something fishy' indicators.)
- Picking Control or Synthesis represents enough of a break of Shepard's will that the usual indoctrination will do the rest. (Although, of course, this 'usual indoctrination' isn't shown.)
And you conclude all of that from a handful of scattered signs that 'something fishy might be happening', and the fact that Control and Synthesis don't feel right? 2 and 4 have nothing in-game to support them, while 1 and 3 have only scant indicators.
Well, it's a theory, I guess. I don't feel that there's anywhere near enough evidence behind it, especially since all the evidence is of the 'something fishy' variety with nothing conclusive, but I can't actually disprove it.
Then again, I can't disprove the theory that the world was made last Thursday either. And personally, I still feel that taking the ending at face value makes more sense, based on the evidence.
Well for 1. There are many scenarios when Shepard could have picked up a small little tid bit, but ya basically arrival would be ideal and to say at least playing arrival makes sense. Rapid Indoctrination is possible, but this would destroy Shepard's mind if it was the case, yet we have to taken in a factor that the collector base had a lot of Reaper tech, it is likely there it could have taken hold. However we also have to take in the factor that the war and when Shepard was on Earth was a total of 9 months. So slowly Shepard could have began to see things, hence the child with in at least at the end of 3 months prior after arrival or SC mission.
2. All sides have been wanting Shepard for their own needs. Shepard has done the impossible, yet is still kill-able and can be mentally brought down despite his/her upgrades. It's possible given how tough Shepard is, the normal approach would not work against Shepard. They need to weaken Shepard to the point he/she is easy to gain accesses too. Which would requier another way. Still speculations.
3. Pretty much, that is when ME3 becomes a horrible mess of sorts, and weird things happen. Harbinger blast scene is what many ITers believe when Shepard starts to go into a dream like state after nearly getting blasted, and pushed back into the rubble, still speculations.
4. Well given on what we speculated in the past the gun represents Shepard's fighting desire. You see Shepard drop the gun in control and synthesis, and in Refuse lower his/her gun as in the fight is over. In Destroy however the gun is being use to blow up the tube and you see Shepard regain his/her strength each time he/she fires. I know in Synthesis Shepard begins to run in a last leap of faith yet for Destroy it shows more of not going to give up just yet feels. Moreover in control and synthesis when you see the two soldiers fighting the onslaught of husk, they get overrun and one of the soldiers hides in fear, while the other one is pinned down. In Destroy however The two soldiers stand their ground, and before the husk can even touch them, the wave destroys the husk. It is all about symbolism, and how in Destroy you see more of a "victory win" rather than in control and for sure synthesis. Plus there is the fact Shepard is being implanted with Reaper tech in synthesis and control. Though yes the eyes are common in synthetics, for people who are infected with Reaper tech, they have the three circles under their eyes. when Shepard is turning into data in both of the two endings, Shepard gains similar eyes as Saren did and TIM. Though it is debatable because Shepard is also a synthetic as well, Renegade Shepard if you go full, has red eyes, yet does not show any indication of the little circles prior to control and synthesis endings. Overall it just depends on what you make of it.
We have supporting things to back us up, yet are we a 100 percent right, maybe ,maybe not. If one comes up with something that contradicts the other, then the one that is being contradicted will have to have higher evidence to back them up to either out way the other, or simply meet the level the other is at. In truth no side has real evidence other than how they view the game, however both sides can point out how this scene or wordings may be this or that. Like i said it's all based on how you see it at the end of the game. So I understand where you come from.