I wouldn't use any preposition there, personally.
She isn't the genius you think she is.
However, I would find it okay to use that:
She isn't the genius that you think she is.
These both give the meaning that the speaker believes that the person they are addressing thinks that she is a genius, and the speaker disagrees.
This might be a dialect variation thing (I'm a native speaker of British English), but I would not use who in this context. In other, slightly different contexts, I would use who or that happily, and would say it was 'wrong' to have neither, though I know some dialects would be fine with neither. For example:
I'm the one who called you here.
I'm the one that called you here.
If you just want to say that someone has the wrong impression of someone, you can say:
She's not the woman you think she is.
She's not the woman that you think she is.
That isn't calling out a specific characteristic, just the overall impression. You can also have the same effect with:
She's not who you think she is.
That one can also be used to refer to actual mistaken identity.