A suggestion in a comment by a reader led me to an interesting hypothesis, which eerily fits the facts.

There is a being — I have generally believed it to be the Cylon god and/or master programmer — who appears to several characters as a virtual or “head” character. Baltar sees this being as his Six, but has also seen it in Baltar form. Caprica Six sees this being as a Baltar, because Baltar was her lover. Starbuck saw this being as a Leoben. It’s possible that Tigh is seeing it as Ellen, on top of Caprica Six. Roslin may have seen it as Elosha. There might be more than one mysterious being behind these visions, but let’s posit there’s just one for now.

Let’s imagine this being is the Final Cylon. When D’Anna stepped into the Temple of Five, she saw 5 figures, one of whom led her to beg forgiveness. If the Final Cylon is the entity behind these virtual beings, in what form did she see it? It could be any form, of course, but it might well be the form of her lover, Baltar. (After all, that’s how Caprica Six sees the being, also as her lover.) And she would apologize to him, and then tell Cavil that “there are five other Cylons” which she would not do if she saw a Six or Leoben or Eight.

She thinks it’s Baltar, but it’s not. It’s virtual Baltar she saw. But she tells real Baltar “you were right” about his claim that he’s a Cylon. But he’s wrong — though he is still the chosen one. Virtual Six has told him that she and Baltar will be parents of the new race.

When she awakes, she shows the most concern for Baltar. Of course, that could be because they were lovers, but it seems like more. And then she tells Roslin “There are Four in your Fleet.” She knows this because she thinks it’s Baltar. She is right, though, there are only four in the fleet.

Now this also jibes with a lot of clues

• Virtual Being has been around since the miniseries.
• Virtual Being is almost always played by a regular, not a guest star. Moore ruled out Guest Stars
• In a sense, Virtual Being is a regular, and one of the most popular characters on the show thanks to being mostly played by Helfer and Callis.
• Fits very well with the “You have heard my voice many times but don’t know my name” clue.
• Virtual Being is potentially not in the “Last Supper” photo, if you take the central Six there to be Caprica Six. She does look like Virtual Six, particularly in how Baltar looks at her and her dress, but this would be a clever trick. Virtual Six and original Caprica six are identical in appearance, of course.
• It’s a shocker. But it explains things. Virtual Being is “The one who programmed us” that D’Anna talks about before being boxed. The one pulling the strings. The one who took Starbuck to Earth and triggered the four Cylons to awaken.
• Virtual Baltar can be (a form of) the final Cylon while Baltar is still human or has another role.
• Virtual Being has physical powers, possibly becoming Shelley Godfrey, and picking up Baltar when he’s down.
• Virtual Being is not asleep however, so Gaeta’s song does not jibe.
• Of all the regulars — indeed of all the significant characters, Virtual Being is the only one fans don’t suspect of being the final Cylon. We keep being told by series insiders that “nobody” is guessing right.
• We’re also told that the ending makes it all make sense, that though they admit they wrote the ending later, it seems like it’s been planned from the start. Virtual Being has been a central show mystery from the start.
• It does not mesh well with the First Hybrid’s line about the “fifth, still in shadow” clawing for the light and seeking redemption.
• In a deleted scene, we see Virtual Six saying goodbye to Baltar. He won’t be seeing her any more. Would this highly popular character vanish from the series conclusion? Or does she move on to a more interesting role? She does say “other angels will light your path.”

Why don’t fans suspect it? Because they already thought of Virtual Being as a Cylon from the start, because for so long it was in the form of Six. But Virtual Being clearly is not one of the 7 Cylons in any way, but has been using Baltar for its own agenda. Virtual Being’s status as a Cylon is hidden in plain sight.

Food for thought, considering how slim the other choices, are, with Ellen Tigh currently in the lead.