What makes the sequencing of Watson's genome different from that of Venter's?

It's the technology. Watson's genome was sequenced using one of the next generation sequencing technologies (454), which allows much more sequencing bang for the buck. This isn't a $1000 genome, but it's a step in that direction. The real value of Watson's genome sequence is a proof of principle. This project was completed at a low cost (relative to the previous methods of sequencing genome), but with high quality. They were able to identify not only sequence variation between Watson and the reference genomes, but also structural variation. To truly realize the potentials of personal genomics, we need many more of these genomes, with the phenotypic data on the individuals.

Along with the article, Nature has published a News and Views piece on the Watson genome paper. The article takes many steps to point out that, while we are at the cusp of an era of personal genomics, there are many limitations as to what we can do with these data. Given our current knowledge, we can't say much about Watson's phenotype that we didn't already know based on non-genomic information. Personal genomics needs not only data, but also ways of assigning genomic variants to particular phenotypes. At this point, we're probably limited to advising a couple about the risks that their child will acquire a particular genetic disease based on sequencing of the mother and father's genomes.