I really do think the indoctrination theory is the 'correct' ending, cause think about what you get when you get 100% readiness and all that business. You're honestly going to tell me that little snippet is all you get for all the work you would put into getting 100%? I honestly think this was a last ditch effort to exploit cash out of the fans of the series. The 'best way' to get some cash flow in from anyone is to 'with hold' the 'true ending' and make it dlc.
As disappointed as people are, people are going to want to see it and are most likely willing to pay for it considering how much time a lot of us put into the series. I only finished the game last night, so forgive me if someone has already said this in the comments. But with the rest of the game, I was pretty please with how everything was working out between the galaxy and the characters. I find it really hard to believe that the lackluster ending that we have is what was really intended, considering all the stuff that leads up to it.
It is a really shitty end and business practice model to a series that was really worth playing the whole way through, such a shame.