This is quite interesting. I see that the Zuk et al paper chose not to model fitness as additive. That is fascinating! I teach Labs for a graduate course on population genetics. We are very careful to mention repeatedly in class when going over the various models that models assuming additivity are but one type of model, and there may yet be others that make more sense that don't assume additivity. Jon Seger, working in whale lice, has found that weakly deleterious mutations might account for a vast amount of the so-called "missing" heritability. It's just so small we won't find it very easy. Lately he's come up with some interesting toy models to figure out how we could see signals of these purported common alleles that should have an (almost!) immeasurably small effect on fitness.

S.V. Nuzhdin and his collaborators have come up with an interesting way of making genotype-to-phenotype maps using structural equation models. It seems like a reasonable way to go beyond GWAS and actually start to pinpoint the exact genes and regulatory regions that work with our environment to determine phenotype.