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They recognize that Sora is capable of a lot, that's why they tried to forcefully indoctrinate him, but they also see him as a sort of "accident" since well...he is. Sora was never meant to get the Keyblade. He was lucky and everything he managed to do was because he had a strong support team behind him. Where Xehanort was able to break up Terra's, Aqua's, and Ven's friendship and manipulate them for example, he couldn't do the same with Sora. Sora draws his power from his relationships and that's what has kept him afloat for so long despite being an island bumpkin with no formal training.

Sora is strong in his own right, but even Yen Sid had to point out that his methods are uncouth and he's still significantly behind Master Xehanort.

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