Well well well........
Not sure if people have seen this yet; but I'll slot this as a big piece of evidence to my theory....
http://social.biowar...ndex/11940879/1
Those that won't actually go and read it....
http://www.youtube.c...g5xltLkk#t=291s
This is an interview from ComicCon 2011 with ME3 Producer Jesse Houston.
"I can't tell you that the end of the story will be on the disc... But
within that context, given the terms there's a bit of a different.. the
way that we're structuring the story is pretty different.. So it will
make a good sense why the dlc plugs in to where it does."
Which confirms exactly what we've seen from the old source code that the game does a DLC check immediately after the "Shepard Lives" ending.
So, assuming plans haven't been wildly altered (and given that bioware is actively making an ending DLC that seems likely) then the indoctrination theory is, in all likelyhood, probably largely right.
As I was saying - lots thought I was/am mad for my theory