Ok, so I'm tentatively returning to the IT thread after playing through the EC with my second character today and choosing Control. I have a lot to catch up on here, but let me just relay my own thoughts and experience first.
With this character, I had played through ME3 completely expecting IT for the EC, and wanted it to have a game where Shep fell for the Indoctrination, because I was sure that if the EC expanded on IT like I had hoped, then the indoctrination choices would not be critical mission failures, but would continue with an indoctrinated Shep.
Anyway, when I first played through the EC with my main Shep, I saw the changes to the ending sequence with the crew evac and the epilogues, and I thought "ok, IT is hollowed out, Bioware's made its choice". Needless to say I was disappointed. I chose Destroy, saw the breath scene still in there, but essentially worked into the epilogue with the crew memorial. Again, I assumed, this was shutting down IT.
But after playing it today and watching the Control ending, I'm beginning to rethink it.
Do I think that Bioware is going to give us any more content on Indoctrination? No. That is what I thought the EC was going to be, and they have decided against it. I do not see them ever addressing IT again, in game or publically.
However, I am rethinking that the EC can in fact coexist with an Indoctrination Theory interpretation of it. I'm guessing you guys are all way ahead of me on this, but the changes in the EC don't fully discount IT. Sticking with the idea that everything after the Harbinger beam is an indoctrination attempt, then there is only one element which has changed; the crew evac.
Now, the missing crew and their later appearance on dream planet in the EC was as continuity error as continuity errors get, and solid evidence for IT. The evacuation scene changes that evidence, after the fact, in order to have the literal ending make some degree of sense. However, it does not necessarily discount IT.
In this version, Shep has his crew evacuated, and is then hit by the beam. When he wakes up, he is then obviously not looking for his comrades or thinking about where they have gone, because he knows they've been taken onto the Normandy. In the original version, this was just weird, because we had no idea what happened to them. However, if going by classic IT, everything post-beam is still and Indoctrination attempt, then everything that still transpires - including the choices and the extensive epilogues, can be said to be part of the indoctrination hallucination that Shep is imagining; seeing the galaxy as he imagines it to be had he taken that choice, just like how a dream operates.
The LI or someone else hesitating to place Shep's name on the memorial doesn't have to be taken as literally happening, but rather symbollically within Shepard's mind, because there is that glimmer of hope that Shep is still alive and awaking, which happens immediately afterwards in the breath scene.
The breath scene is still an issue; is it on London? The Citadel? Can it still accomodate Indoctrination Theory? If it can, then IT is still a completel valid interpretation, because there is still an extremely solid case for it, even coexisting with the new more literal friendly EC ending.
Thus, to cut a long story short, my hope has been rekindled... It isn't what I wanted, but for now, it's enough.