The gene may be the key to the protein but the protein is the key to the phenotype.
That is only half of the recipe. The pattern of gene expression, the trascriptome, is just as important. When a protein is expressed during development, maturation, and environmental challenge also has impact on phenotype.
For example, some studies have suggested that overexpression of anti-oxidant enzymes can increase lifespans. I can't find the reference now, but I am pretty sure that this has been done in mice.
Mapping the genome was the easy part. Understanding the proteomics of gene alteration is many orders of magnitude beyond that.
Fully agree. Just figuring out which genes produce which proteins is a small step. You still have to understand how those proteins are modified by other proteins, alternately spliced mRNA products for the same protein, etc.