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Seriously?
I don't think the character was ruined at all. There's nothing wrong with showing a bit more emotion for her, Samus never seemed like the ''machine'' character to me, I knew she was always a human, and everytime I saw those endings that showed her in her zero suit, I could see it was a being with emotion.
I'm sorry but I never saw her actually CRYING, she may have made a small whimper, but there was not a damn moment in which she fell on her knees and CRIED.
And Adam's reaction helped things, he was shocked to see what was going on. If anything, he must have thought something was wrong with her suit instead of a mental issue.
Although Samus waiting for orders and permission to use some weapons by Adam does bother me slightly...
I guess this is her military way of thinking, since he was her commander. I'm guessing she thought: ''Alright, I'm sure he knows what he's doing and I trust him, I've always trusted him.''