Here goes.
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Sid. I’d say so. We don’t exactly know what happens to him after the events of Toy Story, other than that he became a garbage man who retains his younger self’s taste in music. Was he scarred for life? Did he grow to respect toys or just fear them? How is his relationship with his sister? Etc. Side wasn’t evil, though. I’d define him more as lost. But it’s not like he was injured or anything. I say fair.
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Hopper. Considering his actions, it seems fair. He went out of his way to hurt Flik and other ants, and exploit them for food. He put himself in a situation to get eaten. And, hey, he contributed to the food chain!
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Stinky Pete. Wasn’t there some profile that stated that Stinky Pete eventually settled down, content with his new life? Pete wasn’t evil, he just was never used as an actual toy. He may have been uncomfortable initially, but he was able to change. Al wasn’t evil, just greedy. But his actions and personality were terrible. Losing his way to wealth was deserved.
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Randall. This one is touchy. I understand the arguments against his punishment, but at the same time, I can see why Mike and Sully did what they did (especially considering them being make-shift guardians to Boo). Randall did, after all, help to banish them and admitted to Sully that he had wanted to kill him for the longest time…before trying to actually kill him… It is possible for him to find his redemption, but he has some serious issues to work through. And at least he wasn’t killed.
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None, really. Maybe Darla, but I wouldn’t consider her much of a villain. More like an immature girl whose parents/guardians/adult figures never taught her how to properly handle a fish.
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Syndrome. While Mr. Incredible’s actions to Buddy were rather harsh, it doesn’t give him the excuse to kill. Buddy’s state of mind probably decayed to that level and he became a murderous, evil villain. I consider him another character that put himself in a position to be killed. After his failed attempt at destroying-and-saving the city, he could have given up, gone into hiding, turned himself in. But instead he went after Jack-Jack, an innocent baby, and flew off. Deserved.
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Chick Hicks. Not evil, but got what he deserved. He won, but the crowd and media disliked his egotistical attitude, preferring Lightning’s genuine heart. Perhaps he simply needs to take a drive and discover himself (much like McQueen).
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Skinner. He got what he wanted, but through that process, Linguini, Remy, and Collette changed for the better. So, he more or less won but still failed.
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Auto. He was simply running on orders, so the blame can’t be placed entirely on him. He’s less human than any of the other robots by far. I don’t see him being turned off as a punishment, but more like turning off a lamp before one heads outside. It was necessarily to return to Earth, and is more symbolic of going against the previous captain’s orders.
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Muntz. Definitely a character that put himself in a position to, well, fall off his air craft and die. Muntz is another mental decay case. He tries to kill an innocent man and child, and capture a mother bird. Muntz kept following Carl and attacking. He shouldn’t be surprised that he fell off at one point.
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Lotso. He was cruel and calculating, and his doomed to be stuck to the front of a truck. A fine enough punishment. Maybe it will give him some time to think. And bond with the other little truck guys.