First, we blokes are, in fact, typically genetically inferior to the fairer sex because of all those hundreds of genes missing from the Y that remain intact on the X. To demonstrate this, one just needs to examine the proportion of men vs. women affected by genetic diseases such as red/green color blindness or the "royal disease" (the hemophilia B-carrying X chromosome passed on to many European royal houses of the 19th century by Queen Victoria) that afflicted the Tsarevich Alexei and entangled his family with the infamous Rasputin. This is because women, with two X chromosomes, essentially have a backup copy for each gene in case one is defective. Men, lacking backups for almost all of their X chromosome genes, are liable to manifest the illness when their one and only copy of the gene is defective.
That said, this paper really addresses the question of whether the few remaining "normal" genes on the Y (excluding those few dealing directly with sex determination, sperm maturation and so forth that are unique to the Y) are just randomly-chosen lucky survivors of eons of genetic carnage (the canonical "rotting Y" theory) or whether their presence is specifically needed on the Y for some reason.
To test this, the team (made up of scientists at the Whitehead, Univ. of Wash. in St. Louis, and Baylor) sequenced the Y chromosomes of a range of mammals, reasoning that if the remaining functional genes on the Y were just randomly-chosen, different sets of genes would survive on the Y chromosomes of different mammals, each having undergone a unique history of genetic change since the species' last common ancestor eons ago. If however, these genes were actually required on the Y in a range of mammals to significantly enhance male fitness vs. not having them on the Y, then the *same* set of genes should have functionally survived on each of the different mammals' Y chromosomes. This latter result is what the team observed; they also observed that this small set of genes is widely expressed throughout the body, even in tissues that do not obviously differ between males and females.
As yet, the functions of these genes are unknown, but they each have cognate counterparts on the X chromosome. Perhaps each gene's Y version has the same function as its cognate X version. However, since the sequences do differ somewhat, there is the intriguing possibility that the Y and X versions *differ* at least somewhat in their specific functionality. The authors speculate that such differences may lead to functional differences between XX and XY versions of cell types that previously had been assumed to function identically in men and woman, and that this may account for some of the observed differences between men and women in e.g. disease susceptibility and other traits. Thus, although we must suffer our burden as the genetically weaker sex, we may yet have some unique traits to salve our wounded senses of self-worth.