So you only believe whatever Bioware tells you and nothing else? As in "this new game will show you what really happened, and you have to believe it without question?". Shepard's story is over with ME3. So anyone who think the new game will pick up after the breath scene with Shepard is fooling themselves. Kind of hard to make a new game where in 98% of the endings Shepard is dead.

Bioware doesn't need to explain the ending being indoctrination. It was quite obvious. Which is why they have not released a DLC stating this. People might say "well the Reapers are still there and the game isn't over". Well, as the link above mentions, you did destroy the Reapers. So essentially goes like this: