Which member of the emerging middle class does Chaucer portray in the most favorable light? In what way does his description of this character differ from other members of this class or estate?

The emerging middle-class were becoming increasingly wealthy and more politically influential in Chaucer's day. It is no surprise, then, to find so many of them represented among the company of pilgrims making their way to Canterbury. In writing The Canterbury Tales, Chaucer set out to present his audience with a cross-section of Medieval English society and so the prominence of the middle-classes in his masterpiece is therefore no accident.
It's largely a matter of opinion, of course, but I would argue that the Clerk is presented in the most sympathetic light among the middle-class pilgrims. He is given to us as a quiet, pensive young man; someone who, unlike his fellow bourgeoise, doesn't feel the need to show off and make himself the center of attention. It's notable that the Clerk doesn't interrupt the others to speak. Nor does he beg the Host to be given an opportunity to tell his story. He simply bides his time until his turn comes.
From his extensive studies the Clerk has understood the importance of Plato's famous saying:

The wise man speaks because he has something to say. The fool speaks because he has to say something.