You guys know about some people are saying that due to some things that occur in the game, and certain tweets from developers that we don't have the real ending yet? And not only that but that perhaps Shepard is indoctrinated? It sounds a bit crazy at first but, consider. The series has a space opera/sci fi military theme to it for the entire series. That is, until you get magically transported up to the citadel's heart or the crucible or whatever and are given a deus ex machina (and depending on what you did through the first 3 games, aren't even given all 3 choices. On my playthrough I was not given the third choice for symbiosis.) Why would all the hours of a realistic sci fi game that the devs put in a lot of work into its lore, suddenly disregard everything you've done up to that point and go really weird on us? Other things to consider:
In the third novel when the reapers are controlling a character, but he snaps out of their hold, it notes that there's a distinct growling noise. While not going so far as to declare that Shepard is indoctrinated, no questions asked, I think we can all agree that the little boy you see get pwnzored just before you escape earth is not real. Otherwise, you'd think someone would see a child struggling to get onto a shuttle and help him up, yet nobody does. Of course you'd also think a Reaper that is not too far away from the Normandy sitting right in front of it and int the line of sight of the shuttles it destroys would also target the Normandy, but that's more likely a convenient plot device.
But before that, when encountering the child in the vent and as Anderson calls for Shepard, there's a strange noise that you could say is a sort of growling noise (note the lack of other ambiance in that scene). When Shepard looks back and the kid is gone from the vent, the noise is heard again. Watch the scene again on youtube and listen for the noise at those parts.
Indoctrination victims are said to see ghostly figures and hear voices. That's exactly what you see and hear in Shepard's 3 dreams. I know hollywood and some games like to give character dreams like that, that are very specific and are very memorable and I myself have never had but maybe once, but Mass Effect generally has a realistic feel to it. For them to suddenly give Shepard, whats the word, lurid? dreams is a bit odd. Also worth noting most indoctrination victims hear voices in their heads while conscious. The only thing Shepard ever experiences while conscious is seeing the kid on earth, who I've been convinced the entire time is not real. And it cannot be a coincidence that the form the Catalyst takes is that of the boy that haunts Shepard throughout the game. How could it appear in a form only Shepard sees unless Shepard is hallucinating, or the Catalyst really is a reaper, perhaps Harbinger (there is a voice behind the voice of the child in the Catalyst scene, similar to the way the rachni talk) that is inside his head? Its logic is also bad.
Why be so mysterious and wipe out organics when the problem they have is with synthetics potentially killing off organics? Perhaps using Sovereign as a representative that warns against creating self aware AI could prevent the problem entirely. Speaking of specific reapers and Harbinger, how is it that he has ZERO lines in the game, and no role in the plot until the end when he blasts everyone trying to reach the beam to the Citadel? Dumb dumb dumb! You talk to a destroyer reaper but not to Harbiner. wat. Oh, there's also unused lines of Joker and some others that seem to hint at having a role in that final battle. The codex says captial ship class reapers are very vulnerable when landed on a planet, so why the hell wouldn't Joker swoop in and blast Harbinger a few times with the Thanix cannon?
As for how Shepard gets indoctrinated, I myself at first thought it was impossible since you have to spend a while near a reaper to get indoctrinated but perhaps all they need is a small chance to get into your head and they can slowly but surely turn you on their side. i.e. a short foray onto a derelict reaper. Also, in the Arrival DLC for ME2 you're knocked unconscious right by a reaper artifact. That has to count for something, although if you don't do that DLC, ME3 claims that a group of commandos were the ones who sent that asteroid into the mass relay. So maybe it doesn't have to count for anything.
A lot of it is wishful thinking perhaps but at the same time, the things certain Bioware devs are saying seem to hint that there's more in store for the game's ending. I sure as hell hope so because the ending is terrible, and has no place in the universe that bioware built up in the first two games. It also has zero replay value if the ending we have is the only ending we'll ever get.
Oh, there's also the curious case of there being number/letter markings in the Catalysts place. If Shepard is the first organic to ever reach that place, why would it need letter/number markings on it? I even noticed this was odd even before I finished the game the first time through.
Right here in the background. 1M1. Would be very odd if its just an oversight, not sure if that texture appears at any other point in the game.