2. At Least A Nod To The Indoctrination Theory... And Perhaps More
Back in April, Bioware had a panel at PAX East and the most interesting thing to note was that when asked point blank about whether or not the Indoctrination Theory was accurate the response was basically "no comment". More specifically it was stated that "We want the content to speak for itself, and we'll let it do so." It's also important to note, that if the extended cut actually revealed that Shepard was indoctrinated, then it wouldn't technically be a 'new' ending. This would be a way to "clarify" and "expand" on the current ending which would still have happened even if only in Shep's mind. Of course this could all be a lot of wishful thinking brought on by fandom still being in the denial phase of 'bad ending' grief. If that's the case, it's still possible that Bioware might throw in a reference acknowledging the theory. If nothing else it'd serve as a final way to clarify that it's not true. While there's the risk of it coming of as rather tacky, don't be surprised if someone like Joker says "No way could Shepard have decided to do that. He must have been indoctrinated!" while someone else (let's say Liara) can respond with "Sadly, it seems that it was the only thing Shepard could do. He was definitely in his right mind."