A very interesting talk at the Library of Congress making a good case for a Greek-Phrygian-Armenian clade within the Indo-European family.
Of course the testimony of Herodotus is -at least for me- the most convincing argument for an ultimately Balkan origin of the Phrygo-Armenians.
Modern Armenians are quite distinct from modern populations of the Balkans but who knows how both they and the populations of the Balkans have changed since the beginning of the Iron Age when the Phrygians established themselves in Asia Minor?
The recent study by Hellenthal et al. did not find any good evidence for recent admixture in Armenians but this might be due to (i) Armenians being unmixed descendants of Proto-Armenians, (ii) Armenians being near-unmixed descendants of pre-Armenians, or (iii) the method not having enough power to detect admixture.
My guess is that the relative remoteness of the Armenian highlands coupled with the heterodox position of the Armenian church hindered substantial gene flow into the Armenian population over at least the last 1,500 years.