I think this is an overstatement. There are elements to the proposed EES that are real and important for biology and evolution. For those elements, the only real controversy is whether labelling them as part of a new synthesis is anything more than marketing; if they change the evolutionary paradigm, then the change has already happened (and most researchers didn't notice).
Other proposed components strike me as being quite variable in their importance. My off-the-cuff take on some of them . . .
Evo-devo: a major, important research program that's already well-accepted and flourishing. Maybe it should be better incorporated into straight evolutionary theory -- but lots of subfields would benefit from more communication with other subfields. (And of no relevance to most organisms, of course.)
Facilitated variation: really an application of some evo-devo-related ideas, and a useful heuristic way of thinking about possible evolutionary trajectories.
Transgenerational epigenetic inheritance: real and unlikely to be of much evolutionary significance.
(Horizontal gene transfer, neutral theory: important extensions to the original synthesis, at least for subsets of organisms, but so well accepted and incorporated that they are not usually mentioned in EES discussions.)
Newman's dynamical patterning stuff: intriguing possibility for early animal evolution, quite speculative and difficult to test.
Niche inheritance: makes me sleepy.
Epigenetic innovation: In the broad sense of phenotypic plasticity, real and important for facilitating evolution, but not very novel. In the narrow sense of an entire population changing phenotype because of environmental change, speculative and poorly supported.
I could easily be wrong about some of these ideas. That's partly because none of them, even the ones I think are valid and important, have any discernible effect on the kind of studies I have worked on -- and this despite the fact that quite of bit of my work has intersected with evolution in one way or another.