The different minhagim go back at least to the separation between Bavel and Eretz Yisrael which goes back to Bayis Sheini. However the pot is constantly mixed as communities move around and intermarry. Note how the Arizel was a mixture, and his minhag is the basis for all hasidic nusachs, and mixes aspects from different mnhagim.
Linguistically, the temanim are probably the most authentic since they pronounce all the nekudas and dageshim, which no one else still does, but its clear Hebrew must have been pronounced that way since the mesoret includes the dageshim that everyone else ignores (e.g. a gimel or daled, with or without a dagesh).