but that "main message" is still dominant, which had the (predictable, in hindsight) effect that some people thought Synthesis meant indoctrination.
It's not just that, it's also the simple fact that the catalyst's explanation, as well as EDI's epilogue contains every buzz word and buzz phrase we ever learned about the state of existence and the goal of the Reapers. Plus the fact that Harbinger spends an entire game explaining to you how the Reapers are our genetic destiny, how we will 'become as they are', 'embrace perfection', 'relinquish our form to them', etcetera. Not to mention "Struggle if you wish, your mind will be mine."
Storing the "essence" of a species (EDI's explanation of the human Reaper), synthesis taking Shepard's "essence"
Organics being "perfected" ("Embrace perfection")
Reaching a "level of existence we cannot even imagine" (EDI echoing Sovereign's words in the epilogue)
Synthesis is the "final evolution of life", Sovereign saying the Reapers are the pinnacle of evolution, Saren saying he is a vision of the future, the evolution of all organic life (organic and machine intertwined, etcetera), the fact that Reapers themselves are a synthesis of organic and machine.
That stuff just has all my alarm bells going off. The way I see it, the catalyst isn't even lying when he explains synthesis, it's simply an incredibly euphemistic / sugar coated way of telling us we'll be harvested and ascended to Reaper form. Synthesis achieves what Sovereign stated was the Reapers' purpose: impose order on the chaos of organic evolution, because it is the so called "final evolution". (Even though every sane person knows there is no such thing as a "final evolution of life" because evolution never stops)
And then there's Mordin with his beautiful explanation of what happened to the Protheans.
Mordin: "Early stages similar to indoctrination. Can guess captured protheans lost intelligence over several cloned generations. Cybernetic augmentation widespread afterward. As protheans failed, Reapers added tech to compensate. Mental capacity almost gone, replaced by overworked sensory input, transfers. Transmitting data to masters. No glands, replaced by tech. No digestive system, replaced by tech. No soul, replaced by tech. Whatever they were, gone forever. Understand now? No art, no culture, closer to husks than slaves, tools for Reapers. Protheans dead, Collectors just final insult."
I mean, come on. The writing's on the wall.