Austen, in Emma, deliberately set out to create, "A heroine whom no one but myself will much like." She's rich, spoilt, conceited, arrogant and that is the point. She has to learn, change, develop in order to 'win' Mr Knightley. Again, unlike Fanny Price, she develops as a character and is forced to realise that she has behaved like a fool - and in doing so, realises she nearly lost the person who she hadn't even realised she loved.
And I don't think that she is particularly mean to Charlotte. Charlotte makes a prudent and pragmatic decision to marry an idiot for security. However, although she mocks the 'courtship' of the couple, she doesn't mock Charlotte once she's married. Instead she shows that Charlotte has made the situation work for her, and, indeed, seems to at least somewhat, admire the way that Charlotte has managed to establish herself in a comfortable home but has orchestrated it that she can avoid her pompous idiot of a husband much of the time! I like Charlotte more on each re-read tbh, but I like her even better as a zombie, in the parody. 