I've never played any of these games but I find this discussion fascinating. I've been ignoring spoiler warnings and just reading everything, and I've followed several links to discussions elsewhere.
Without knowing the full context, I feel like there was at least one writer pushing for the "indoctrination" ending, and at least one writer pushing against it, resulting in the messy ambiguity present in the current ending. It's like somebody wrote a draft that was set in Shepard's mind and then somebody else wrote the next draft without being aware of that context. I'm coming from nowhere on that though so I don't know if that could really be the case or not.
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"I think it's the idea that counts, not the actual method. As long as you set out to cause a horrible death through insects eating the person, you're good." - apenpaap
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