Sorry to bring this old thread of mine back up, but I've been doing alot of research lately on the Komnenian Army and have increasingly come to the conclusion that they did indeed re-establish the Theme system in most of their border regions, but seem to have created these provinces as units of "stall troops" in the tradition of the Late Antique Limitanei, in Anna Komnene, Choniates and later texts relating to the Empire of Nicaea, the following themes with local troops can be identified:
East:
Theme of Neokastra
Theme of Opsikon/Optimates
Theme of Paphlagonia
Theme of Chaldia/Trebizond
Theme of Mylassa and Melanudion (in Caria)
West:
Theme of Paristrion
Theme of Nis/Branicevo
Theme of Sardika
Theme ofDyarrachion
Theme of Scopia
Theme of Phillipipolis
The Naval units of the Empire were definitely raised from Hellas, Crete, Cyprus etc...ie: under the command of the Megas Doux, the commander of the fleet. As "stall troops", these Komnenian Themes were likely mostly infantry, and were used for local garrisons, policing and defense. The cavalry of the army, however, were fully "Tagmataized" (I know, not a word) and were recruited from the core territories such as Thrace and Bithynia.
So overall, my thesis is that the Komnenoi's reforms of the army ended up resembling the army of Justinian in organization...albeit on a much smaller scale in terms of numbers and territory. If this is totally crazy, feel free to let me know, just some conclusions I came to after a few months of intensive research partially inspired by the great minds on this site!