erm, I have one view point not to sure whether it has been mentioned, but it gives hints to indoctrination as well, go back to the arrival DLC. From Mass Effect 2. Shepard the indoctrination process starts there, as he has contact with that reaper pylon thing.
Also the dream sequences, we see it as nightmares, perhaps its the indoctrinations trying to destroy Shepard willpower? Since that his strength which is willpower.
Also the games in terms of DLC's well they cant really go back and do DLC's they have to start of from where ME3 (the current game) ends. Otherwise it will effect any ending so it is possible that this is not the "REAL" ending.
And maybe at the end when he sees harbinger the power of it completely takes him over and its a matter of wills, and that is what we see.
Also another point to mention the Illusive man he also wants to control the reapers and uses that, but we al know he is somehow indoctrinated based on the books/comics, and the eyes. Look at Saren aswell form Mass Effect 1. He also was indoctrinated and sided with the Reapers to benefit it. And it ties in to the Reapers Plans.
I support the indoctrination theory as it is plausible. And if you look starting from Mass Effect 2 right until ME3 you can find it. Arrival, Saren, Illusive man, anyone in contact with reaper things get somehow indoctrinated or slowly indoctrinated. It allows you to feel what you doing is right. And it also for Bioware and EA opens doors to DLC's and for a Mass Effect 4. which will be like a spin off to this trilogy of Shepard's.
Also Bioware planned it. At the end the boy says to the grandpa "When can I go to the stars". They also not on Earth by the way.(the moons) and "what will I find". He responds wherever your imagination takes you.
Now look at it as if he is telling us that.