Again, do you seriously think that Bioware is capable of doing this? Given Tali's stock photo and Joker's sudden urge to go relay jumping (Ride the Flavor Wave! with your choice of lime, cherry, or blue raspberry!), the ending just screams laziness.
In the end, the indoctrination theory is just a "it's all a dream" theory. It's not necessarily a bad thing; Inception and Total Recall handle it well, mostly because those two films are built around the questioning of reality. In Mass Effect, it's there, but it's not really prominent.
Still, even if it were true, with the prevailing theory that everything after the red beam is a dream, Shep's still on Earth taking a nap (or dead) while everyone is dying around him. He failed.
The stock photo was lazy, but on the whole, a lot of work obviously went into this game. (Edit: Oh, and I'm not looking into the Joker thing too much right now, because if the indoctrination theory is true, then that didn't happen. Shepard wakes up after the Normandy lands on that planet, so Shepard was still hallucinating at the time.)
FrontalMonk responded to your second point pretty well, I think. So I have nothing to add.
And I don't necessarily think Shepard failed (yet) if s/he went with the Destroy ending. I doubt Shepard was knocked out so long the Reapers had time to finish the entire battle and leave. (Edit: The Reapers had been assaulting Earth throughout the entire game, and still hadn't finished up yet.)
If he were indoctrinated, why wouldnt the prothean vi at thessia know? It detected Kai leng. So you have to assert Shepard was "corrupted" between thessia and earth.
Just doesn't sit right with me.
That's the one thing that didn't make sense to me, but I noticed on Earth near Liara there's a datapad from the point of view of someone that seems to be undergoing indoctrination while on Earth. So Shepard being indoctrinated while on Earth apparently isn't impossible, and maybe even foreshadowed.
Also, Shepard ends up fairly close to the Reaper you kill after fighting all the Banshees. Maybe that was enough combined with previous exposure to Reaper tech to indoctrinate him/her.
Yea. That's brilliant.
Also having the high EMS makes the kid say, "Wake up" instead of "why are you here?" is pretty trippy indeed.
That's pretty cool. I never would have noticed that myself.