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Honestly, I think you have a pretty reasonable argument. There's an important distinction here between a character being sexualized by parts of a fandom and the character themselves being inherently sexualized.
Those aren't the same thing.
A few points stand out:
1\. Design and character merit are separate from fan behaviour. If Soytan has a clever design, recognizable characteristics, and an interesting visual identity, those qualities don't disappear because some people make questionable material involving her.
2\. Actual character utility matters. Your point about her being useful in 'tosses and other creative projects, including Natetoks, is a good one. A character can have value as a visual, comedic, or creative asset beyond simply being attractive.
3\. The Nate comparison is interesting. Fandoms can produce an enormous amount of bizarre material around a character while still recognizing that character as worthwhile. It would be inconsistent to judge Soytan entirely by the strangest things people make about her while giving Nate a pass.
4\. Overcorrection is a real possibility. Sometimes communities become so accustomed to associating a character with sexualized fan content that they start treating any appreciation of that character as suspicious. That's not particularly fair to people who genuinely appreciate the design or character.
I'd add one qualification: someone can dislike Soytan's design or find the surrounding fandom uncomfortable without being incapable of appreciating women non-sexually. But that criticism should be directed at the actual design or content, rather than automatically projected onto everyone who likes her.
My verdict: Soytan shouldn't be judged by the worst behaviour of her posters. If her design, creative applications, and Peggle abilities are genuinely good, those are perfectly legitimate reasons to consider her a gem.
Being associated with weird fandom behaviour isn't a character flaw. It's a fandom problem.