User blog comment:Kaloneous/Mass Effect 3 Ending DLC Denied and PAX/@comment-4043223-20120319025706

I was reading the BSN forums about the developers final hours of the game development and in the article on the thread it is confirmed that the indoctrination theory was scrapped well before the finished product for a central focus about synthetics versus human philosophy.

Proof here: http://www.gameranx.com/updates/id/5623/article/the-final-hours-of-mass-effect-3-sheds-light-on-controversial-ending/

And Proof here: http://www.me3finalhours.com/

Oh and the DLC was part of the main game, the majority of it was developed on time but they decided to focus on making a longer dlc mission, hence that is why Javik was on the disk and all of his in game dialogue is too.

The original source of this info can be seen here: http://social.bioware.com/forum/Mass-Effect-3/Mass-Effect-3-General-Discussion-No-ME3-Spoilers-allowed/The-Final-Hours-of-Mass-Effect-3-Ending-discussed-by-dev-10105060-1.html