User blog comment:AdmiralPedro1stFleet/Goodbye Indoctrination and Hello Beings of Light/@comment-1345979-20120419025742/@comment-5017885-20120419041009

I don't recall any of the BioWare writing staff actually stating matter of factly that Indoctrination Theory is false: others have said it before, and I'm also taken to believing that, as they are the writing genii we know them to be, the writing staff may very well have planned Indoctrination Theory from the get go, but been unable to implement it fully due to myriad constraints. You can feel that the game started rushing to the end at Thessia, so it's not unreasonable to assume that a proper conclusion could not be included due to time constraints, and it's also not entirely unreasonable to assume that the decision to "keep the current ending" is one not made by the writing staff.