PixlBit

So you only believe whatever Bioware tells you and nothing else? As in "this new game will show you what really happened, and you have to believe it without question?". Shepard's story is over with ME3. So anyone who think the new game will pick up after the breath scene with Shepard is fooling themselves. Kind of hard to make a new game where in 98% of the endings Shepard is dead.

Seriously though, I've done my homework. Some people would rather stand around for 2 years waiting for answers (eg. you, many others), while the rest of us did something constructive and put the pieces together. Everyone else just wants instant answers with no effort on their part.

They say it's bad writing that the ending is poorly explained or "doesn't make sense", but the answers were there all along. 

Don't hate because the meaning isn't handed to you on a silver platter. This game has always been about choices and consequences. If people choose not to pick up on the clues and such, then you will be rewarded with a bad ending. If people paid attention during the game, then you will get a good ending (Bioware indoctrinated you).  They had no plans to reward those who didn't pay attention during the game with the answers. If you want a good ending, you have to work for it. It's a little change from the previous games where Bioware essentially did most of the work for you, but without innovation and new ideas, any game would get stale and boring.

Bioware doesn't need to explain the ending being indoctrination. It was quite obvious. Which is why they have not released a DLC stating this. People might say "well the Reapers are still there and the game isn't over". Well, as the link above mentions, you did destroy the Reapers. So essentially goes like this:

Shepard shoots tube, Reapers destroyed, wakes up on Earth. Reapers dead, you win.

Shepard was never on the Citadel. He was on Earth the entire time, and the last 20 minutes or so took place in his mind. 

Certainly does jive with something Harbinger said during Arrival (Struggle if you wish your mind will be mine). 

Codex states: Reaper indoctrination is an insidious means of corrupting organic minds. 

Extended Cut was a mere extension of the original illusion. The extra slides take place before you wake up, as Shepard is just imagining these things. Your squadmates never actually go back home. Actually according to the codex, if the Reapers are not defeated, Harbinger uses your squadmates for slave labor. The cutscene you see in the new synthesis ending is just that. Reapers aren't helping you rebuild. They have enslaved you. 

In control, Shepard becomes loyal to the Reapers, and anyone who tries to destroy the Reapers will be destroyed. 

EDI: We may transcend mortality itself. Harbinger: Thank us, beg us for immortality. EDI: To reach a level of existence I cannot even imagine. Harbinger: Your species will be razed to a new existence. 

EDI=Indoctrinated. 

Shepard: ...only achieve this by becoming something greater. Harbinger: Your species will be razed to a new existence. Shepard: Eternal, immortal, infinite. Harbinger: Thank us, beg us, for immortality. Shepard: I will destroy those to threaten the future of the many (Reapers). EDI: We are Legion (ME2). Sovereign: We are Legion. 

Shepard=Indoctrinated. 

Also, the Final Hours app states that anyone in Synthesis gets Reaper DNA. While as we saw during the game, that the Protheans tried to control the Reapers, and became indoctrinated. 

Pretty self-explanatory. Was never going to be an obvious yes or no answer to whether indoctrination was the case. Indoctrination has been subtle since the first game, as it was very subtle presented during the original and EC scenes. Most people did not pick up on it. 

That's the thing with subtlety. Stuff that is important to know, but it's not made really obvious. Half the people who played the game didn't even know they were being indoctrinated, while at the end they essentially bowed to the Reapers, and joined their cause. Your mission from the first game has always been to destroy the Reapers. You cannot control the Reapers, and you cannot merge with their DNA. These are tricks that Bioware put in the game to see whether people were paying attention or not. The paragon/renegade switch is another trick to see if you're paying attention or not. Seeing as most people picked control or synthesis, these "paragon" options are actually renegade, because you are helping the Reapers (paragon). While destroying them is a renegade action. 

Seeing as most people just believed whatever the Reapers told them, and didn't pick the destroy option, they've been indoctrinated. 

What a brilliant piece of writing there. Bioware successfully indoctrinated their own customers with an indoctrination ending. Best game ending ever.