GWAS is... well, GWAS is just a technique to find statistical correlations between genotypes and phenotypes. It's a very limited (powerful in one way, but limited in many others) way to approach the problem of "to what extent do mutations in DNA cause phenotype changes". It requires fairly large sample sizes to do reliably for diseases which don't have a really strong (mendelian or otherwise) signal, it's fairly poor at working with pairs or larger # of interactions between genes, can't do much with genes and the environment, and is a really simiplified model of how organismal biology works, anyway.
there are a few issues with exome:
1) exome prep is a big issue in itself
2) exome leaves out large regions which are likely to be important in understanding many aspects of human biology
At this point, I'm speculating:
even whole genome sequence at relatively high coverage per individual * large # of individuals is likely to not explain all the aspects of organismal biology. There appears to be a fair amount of state that is transferred from a parent cell to a child cell during mitosis that is not expressed in our current DNA assemblies. The whole chromosomes themselves are complex, enormous structures that undergo massive rearrangements during the various phases of the cell cycle... yet are still capable of maintaining tons of epigenetic state. Very little or none of this is really being analyzed in a systematic or rigorous way, which is frustrating to see because, as somebody with a training in human molecular biology, all of this has been KNOWN FOR DECADES! I mean seriously, Chapter One of Molecular Cell Biology, please!
Wikipedia says about exome sequencing that's a "cheaper but still effective alternative to whole genome sequencing."
I have some basic knowledge of biology, but I'm don't know anything about sequencing... do you have some details?