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.
That's only part of what the Catalyst claims, but the issue is contradicting the events of the story, not arguing against Shepard. Opinion and perspective of the characters are not relevant to that point.
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.
No. It calls itself a construct because it was made or constructed. If Shepard was just talking to himself, then what actually happens? Is Shepard really up on top of the Citadel? Did he actually activate one of the options? How would he know what did what?
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.
You didn't "figure things out," you created your own answers by selectively grabbing bits and pieces out of the whole. I don't get your point about the camera pan. In the video you posted, the original ending shows a better shot that nobody was behind Shepard. More importantly, Anderson says he's in a different place. That was made explicitly clear. The scene just looks better in the Extended Cut, like better camera work in a movie. Likewise, the kid already told us that he was "the collective intelligence of all Reapers." The voice with Refuse was just an audio cue that it was mad now and done being friendly.
Most importantly from your weird list, we already knew why the kid's opinion was out of place because of the events of the series.
There's no indication that TIM knew what Control actually entailed. He probably thought he'd keep his human form and do to the Reapers whatever he's doing to Shepard and Anderson. Synthesis is not what Saren had in mind, What Saren ended up being is what Saren talked about and that was only to justify allowing Sovereign to implant him with that tech and make it sound like a good idea. And both were Indoctrinated.
However, in a historic and miraculous moment, you're right about one thing. Refuse was set up in the first game, which is why something along those lines would have worked to end the series. However, that option wasn't included at release and in the EC, it's arguably just a middle finger to the player.
The ending only makes sense to you because your understanding of what came before is incorrect, likely because you're trying to force what came earlier to make sense in light of the ending rather than the other way around.
the evolutive speed of synthetics is the problem. We don't have enough info, but the geth in 300 years have evolved from high-tech gardeners/workers to one of the most powerful galactic armies, and they almost reach the dyson sphere level.
Give them other 300 years. Are we sure that they will not automatically win?
If we assume that synthetics are generally able to develope/improve themselves faster than organic, on the long term the (maybe inevitable) conflicts are going to be more and more one sided...
Another thought is that the Geth may have advanced in terms of building into a military power, but there is little indication of advanced technology over the organic species. Their small arms work differently but their other technology is largely the same.
But Peace is only one possible out come.
Either of the other options only prove the Catalysts statement.
Only in 33% of the galaxy's possible realities is the Catalyst wrong
No, the Catalyst says Synthetics will wipe out Organic life. The Catalyst is wrong in all 3 outcomes as the other two are organic victory or synthetic victory and then co-operation with other organics.