This is an excellent start for a long discussion on economics, ethics, psychology, etc. that probably would be done better in a cafe, slowly sipping Earl Grey tea rather than on HN, but still..

One of the main points of the argument is that

   i)   It is feared that the rich will take advantage if this is legalized
   ii)  But the rich already have many ways of access to organs anyway
   iii) It is predominately the poor who die waiting for a kidney.

I think the main argument against explicit sale of kidneys is on moral grounds, nor operational, i.e. how to best implement this system. You are selling part of your body, which no sane person in a normal situation would do, so there must be something wrong with this. This argument runs foul of the fact that other such activity, that is on similar gray (or really dark gray) area, is legal, e.g. prostitution, getting compensated for being a surrogate mother.

Let's zoom on prostitution. You think it may be irrelevant to selling kidneys, but think about it: you are selling something to a stranger, kidney in one, dignity in the other, that normally you would not do. Many countries have legalized prostitution (http://en.wikipedia.org/wiki/Prostitution#Legality) because of the realization that it is not the actual act that should be banned but all the bad secondary factors it brings, i.e. sexual slavery, veneral disease. If these can be controlled, why not make it legal between consensual parties. Still, this doesn't leave me feeling good, I feel an unease that I cannot put a finger as a human being.

I feel similarly for selling organs.

Nonsense. Saying that kidneys should be "commoditized" to avoid the black market it's like saying that slaves should be legal to avoid people travelling in a container.

In particular, kidneys can be transplanted from "dead" to living, and donning between living - even inside your family - is very restricted (at least in Uruguay). Although one case may be very altruistic and reasonable, there are thousands of subtle situations which are horrendous, and all the donning process will be heavily affected.

It's a moral statement: you can't put price on life or your body.

Improving the donors rate with policies is a better way to go and it hasn't reached its limits so far.