mass degeneracy differences
What I am saying is that the reason there is a mass difference within the quark doublets is because flavour symmetry is broken. Isospin up and down are inverse, but no longer completely symmetrical. Charmness and strangeness could be considered inverse to each other, but they are no longer symmetrical. Topness and bottomness may be considered inverse, but they are no longer symmetrical. If there was total symmetry, then you would find the heavier flavors following a pattern where C = -S and T = -B. The up and down quarks would be degenerate in mass, the charm and strange quarks would be degenerate in mass, and the top and bottom quarks would be degenerate in mass.
Now, if there were no other influences, all indications are that flavor would be an exact symmetry of nature, and hence this degeneracy should exist at a limit such that all other forces become null. But we do not live in such a universe.
The up and down quarks are already a fairly good model due to the fact that they are already sufficiently degenerate that we can approximately express both quarks in terms of one flavor only. So we do not have to distinguish between "upness" and "downness" because they are very close to symmetry such that U = -D (approximately). Rather than use the flavor names, we just characterize it by one property, isospin.
Here's the first important question: What is the symmetry breaking mechanism? So far, we have some satisfactory theories; the foremost is already used as if it were a confirmed postulate, and there is alreay a great deal of work built up on it. Basically the idea is that electric charge, also known as electromagnetic symmetry, is the mechanism that breaks flavour symmetry. If you were to allow the Weinberg angle (which characterizes the splitting of weak and electromagnetic forces in the electro-weak regime) to approach a right angle, then the isospin symmetry becomes complete and electric charge dissappears. Hypercharge would be the only remaining component to be acted upon. The nucleons would become degenerate in mass and charge, and the pions would also do the same, as would all of the isospin groups. Also, the quarks would probably not mix; all of the non-diagonal terms in the Cabbibo-Kobayashi-Maskawa matrix would drop to zero, leaving the diagonals at unity. In this model there would be total degeneracy within the heavier flavour doublets, as well (so corresponding kaons and D-mesons would become degenerate, too).
Now, the second question is a bit trickier; I don't know if there is an effective answer yet, unless somebody has theorized that the Higgs field affects the flavour doublets differently based on overall mass (or something like that): Why is the degeneracy different in each doublet? I don't have any clues as yet, so I think that's the question to discuss and get some possible answers to.
