I expressed my opinion in a twitter conversation yesterday that this article is getting attention for its (imo unnecessary) tone and some admittedly good quips. Without those it's just an overview of the conversations amongst bioinformaticians (and much wider) that happened everywhere in September.
Thanks for the link - that makes for an interesting read.
My first instinct is it to disagree with the paper's criticism with regards of the hype and inconsistencies in communicating the summary of the ENCODE findings. I think that is just a byproduct of the way we produce/consume information in this age and we can't really fault any individual for that.
The paper also contains more objective and substantial criticism of the methodology and results. The validity of those still needs to be determined. I think that the conclusions of a project of this magnitude will be (or are already) treated as starting paradigm by a large number of life scientists. Therefore the burden of proof needs to be higher than for other papers - as it affects the direction an entire field of science takes.