Personally, I see two possibilities:
- She's a Seraph/Being of Light like in the original series, and that's that
- She's an avatar of some kind, and the BSG universe is actually a simulation like Caprica's V-world
These two options aren't necessarily mutually exclusive. After watching Caprica, it would not be a huge stretch to take what is learned through V-world and how the Cylons came to be, then extrapolate that the universe that is presented in BSG is just another abstraction layer above V-world.
This would explain the hybrids and their prophecies (perhaps they are hooked into the source code of the universe), and would explain the angels and godlike individuals both in the series and in the backstory.
The key difference between the V-world and the BSG universe would be conscious awareness -- V-world participants have consciousness about their external lives, most of the characters presented in BSG do not, and likely do not have lives outside of the simulation. I would posit that Head Six and Head Baltar have awareness and have existences outside of the simulation, and the being that shall not be named "God" is perhaps the architect of the simulation. Starbuck is something of a glitch, or perhaps had been "installed" by "God", and was sent back after exercising her free will to commit suicide because her role was too important.
This does mean she is literally a Deus Ex Machina entity -- which isn't necessarily a bad thing. I'd hesitate to label anything that can't be understood at face value as "bad writing", not everything can or should be told in a story without abstraction. TV used to be without abstract concepts -- everything was as it was told, and as it has improved as a storytelling media that has begun to melt away and if often incorrectly assumed to be just a result of bad storytelling. I would suggest that her reappearance in season 4 and disappearance at the end of the series is too blatant to be a mistake -- remember, she returned within a few episodes, too few to be a result of fan reaction (plus they filmed her return scene around the same time they filmed her death).
So, take the obvious anomaly that she is to infer something about the universe the story inhabits.