Chuck,
we (Doyle and I) have been discussing this on PEN-L for a day or two. But w.r.t the above, IMHO you are wrong: Natural selection (as per standard theory and the MS) occurs at the level of the individual. Arguments for higher levels of selection, "group selection", have been around at least since Wynne-Edwards (late 50s?), and Gould/PE have little to do with that.
> The depth of its importance comes from the fact that natural
> selection only works through phenotypes. If that's all there is,
> then how do genetic sequences change, how does the genotype change?
> Influence through epigenenome changes provides one answer.
Why do you need epigenetics to explain genotype changes? Drift, random mutation, etc -- the old bag of tricks -- have been around as explanations for a long time. One new problem may be how you explain the diversity in light of the comparatively small number of genes. Here epigenetics could play a part.
I do agree with you that this can be a very significant development in biology. I also share what I believe is your distaste for the gene's eye view of human biology (and often, destiny).
Here is a link I posted on PEN-L that you may find interesting:
http://www.amazon.com/gp/blog/post/PLNK3EC629BEDKT8X
--ravi