One thing that I don't think is explained away so quickly by iodine deficiency is the morphology of the hand and wrist bones. It's just too different.
It seems like there's a group of paleoanthropologists who are looking for any possible reason to disclude the Flores remains as a non- H. sapiens hominin.
Interesting that they also used the stories of the ebu gogo to support their claim of cretinism, but since that cryptid has also been used to support the idea of the hobbits as being a separate species, it seems like a "just so" story and not really supportive of their claims.
A critique quoted from an article in the Sydney Morning Herald:
"Professor Brown, who has examined LB1, said one of the skull features, an unfused area, cited as evidence of cretinism was the result of damage during the excavation.
"The authors have not examined the original fossil, have little and no experience with fossil hominids and depend upon data obtained by others,'' he said.
Dr Groves, who has previously argued Homo floresiensis is a new species, said the new paper also ignored the fact the hobbits had primitive chins unlike those of modern humans, which was not only evident in LB1 but in a second jaw which had been found.
Leader of the discovery team, Mike Morwood, of the University of Wollongong, said the remains of at least 12 hobbits had been found in the cave dating as far back as 95,000 years ago, which was too early for modern humans "normal or pathological'' to have been there."
http://www.smh.com.au/news/science/scientists-clash-over-hobbit-species/2008/03/05/1204402511772.html?page=2