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I think Misaki wants to save the Misaka Sisters because in a way they are similar to herself. With the exception of Touma, the Sisters really can't trust anyone outside of their Network, much like Misaki can't trust anyone outside of hers.
With Misaki's distrustful attitude, I bet she experienced the Dark Side of Academy City more often than Mikoto did when she was growing up and met people who treated her as nothing more than a disposable stepping stone, much like how the participants of the Level 6 experiment treated the Sisters.
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