There’s a nice roundup of the problems faced by current chip-based techniques to find disease-gene associations. This is the technique practiced by 23andme.
Current chip-based technologies for genome-wide analysis, while having some success in identifying the lowest-hanging genetic fruit for many common diseases, seem to have already started to run up against barriers that are unlikely to be overcome by simply increasing sample sizes. These technologies should really be regarded as little more than a place-holder for whole-genome sequencing, which should become affordable enough to use for large-scale association studies within 3-5 years.
Nothing beats a large, diverse library of full sequences. There will be many a position available for the enterprising bioinformaticians needed to compile and interpret this data store.