I decided to move the bulk of the post to the comments.
Before a detailed response, let me see if I can correctly summarize our disagreement. You seem to be claiming that the Modern Synthesis of population genetics with natural selection is defunct, out of favor, discredit, or something similar. I have been saying that the many additional mechanisms we are seeing recently are things that will be incorporated into the Modern Synthesis, and that complement it rather than replace it.
On that topic, consider this link (with a hat tip to Panda’s Thumb).
LH: What are the most exciting recent developments in systematics / comparative methods?
JF: The availability of genome-scale information is certainly one. The arrival of a generation of young researchers who are comfortable with statistical and computational approaches is another. But the most important development is reflected in recent work on coalescent trees of gene copies within trees of species. What this does is tie together between-species molecular evolution and within-species population genetics. Those two lines of work have been developing almost independently since the 1960s. But now, with population samples of sequences at multiple loci in multiple related species, they are coming back together. This is not another Modern Synthesis, but it is a major event that needs a name. How about the "Family Reunion"? Long-estranged relatives who have not been in touch are getting together.