I'll be getting the extended DLC...
Regarding the video, yeah, it did raise a lot of new points which I haven't seen before which supports the Indoctrination Theory.
But I guess the best points which supports this is:
a. Khaidan and Ashley's dead bodies around the Conduit
b. Everything inside the Citadel are the collection of Shepard's memories (Mass Effect 1 1M1, Mass Effect 2 Collector Base and LOTSB, etc.)
c. Indoctrinated eyes (which is present in the guidebook) present for Control and Synthesis choices.
d. "Oily shadows" present in dreams and in the final scene.
e. Inconsistencies (Location where Shepard gets blown up during the run to the Conduit VS when he wakes up, Anderson, TIM, Hackett, etc.)
f. Ghost child (Obviously a Reaper when he says "Us")
g. Shepard only lives with enough EMS for the Destroy option.
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Well, the extended DLC might answer these all, but before getting it, the Indoctrination Theory has got to be the best explanation out there, since you have to admit! Either Bioware is stupid enough to have a lot of logical inconsistencies, or they were all intended.