Everything was done using established elements and knowledge. There was nothing new thrown in at the end. Mass Effect 3 did not do that. You had a completely new character come in claiming things that were new, unfounded, and contrary to the events of the series.
The kid saying that organics and synthetics can't get along isn't contradictory at all. Especially from the Reaper's perspective. He establishes himself as the creator of the Reapers. The Reapers themselves have established previously that they don't believe organics and synthetics can co-exist. Having a different opinion that is completely against what the protagonist stands for would make it the antagonists opinion.
The kid is the antagonist (the Reaper's creator), obviously taking the form of a child. He even says he is a construct. A theoretical entity constructed by your mind. That may or may not be real (by definition).
Shepard might just be talking to himself the whole time.
It's also a silly assertion that a game being about choice (though you don't understand the way in which it was about choice) merits an ambiguous or unexplained ending. The choices and endings were perfectly clear in the previous two entries. The same is true for other games like Dragon Age Origins. Clear consequences or at least knowledge of what they might be, are critical for making an informed decision.
The ending wasn't completely unexplained. It did require you to backtrack to previous games and knowledge to figure things out. The writers didn't feel the need to hold people's hands and explain every little scene in detail.
Did we really need that camera pan in the Extended Cut showing that Anderson wasn't behind me? No, I could have figured it out. Did we really need that Reaper voice when you shoot the kid to reveal his true form (Reaper disguised as a kid)? Probably not. Did I really need to know why the kid's opinion about synthetics and organics was out of place? Nope, because it was exactly what the Reapers have said earlier. It's not hard to figure this stuff out if you think about it a little.
It was previous established in the trilogy what controlling the Reapers was (see Illusive Man). Same goes for synthesis (see Saren). Even refuse was an option (submission not preferable to extinction).
So it's not against the previous established story. It's against what you wanted the story to be about. Same goes for the ending. You wanted a clear-cut ending, with clear-cut choices, because the previous games were like this. While Bioware decided to make this ending ambiguous and vague on purpose. Despite all the criticism and backlash, they stuck to their guns and told you to deal with it.