When I was annotating the Arabidopsis thaliana genome in 1997-1999, fully 95% of the genes we described from genome sequencing and modeling of ab initio-predicted exons were new. Since then, yes, there has been an explosion in building chips and doing all kinds of genome-wide analyses. That work has led to amazing results in differences between cultivars (isolates) of the species (gene expression, methylation patterns, etc.) For this, one can look at the work done by Joe Ecker's lab.
Similarly, in humans, there has been huge advances in technology (the arrays and chips and ability to assess protein and metabolite levels) with concomitant great leaps data points attached to genes. Now, I see that there is a return, to a degree, to the single or small gene set focus. The recent paper by Wasserman et al on GWAS hits far upstream of the MYC oncogene actually affect enhancer activity of that gene.
So, while there are more and more genome-wide studies undertaken, there are also increases in the number of papers looking at specifics of a small number of genes where attention is given to their biological role(s).
Specifically, one way to address the illustration you wish to make could center around a few genes and the number of papers published each year on that gene. Note when the gene was discovered and when its genomic sequence was deduced by that oranisms's genome sequencing project. You could also note on this timeline when certain tools came on-line - such as platforms for whole genome analysis of mRNAs, proteins, methylation patterns, and genome variation.
Like Mary wrote, these are thoughts that just come to mind after a quick thought. These would be better refined in a face-to-face roundtable discussion...
Mary, interesting thoughts, thanks! And even if we disagree on how to do annotation, I think we can agree on the importance of it... ;)