I remember YoshiP saying it would be a combination of Luminous+Crystal Tools in one of the interviews...
Or more like, core programmers of the Luminous engine are also the ones writing the engine for ffxiv, while keeping the compatibility to crystal tools data (our characters)

tbh, that last part is somehow worrying me. They should get away from crystal tools completely and just write a converter for our character data.

Oh and crystaltools is not UE3, it's SE's own development.