Yeah, speculation abound here... I've been soaking up all the info here for the last few weeks, seeing what I can find. I admit being a bonafide lurker, so pardon the low post count. Just thought I'd post a few opinions and random info I've noticed.
First off, I remember someone here posting how a lot of people think the Night Rune and Blue Moon Rune are related. Well, they might... but only because of the facts that the Night Rune allows Vampires to exist, and the Blue Moon Rune turns the bearer into a Vampire.
I'm also curious about the Blue Moon Rune being brought up, because if I remember correctly at this point in the timeline, Neclord should still have it. Are people assuming that Neclord is in this game, or are they just hoping he is? I don't remember seeing any info about the Blue Moon Rune being in V.
As for the three runes, I would have to agree that Sun, Dawn, and Dusk would be the most appropriate. As for how they relate, someone's said that the other two were subservient to the Sun Rune. I am going to make an assumption here and say that the info may not be complete right, and was set in place to make sure that no one tried to defy the Queen, by making the Sun Rune seem unbeatable to all other royal treasures/runes.
Other ideas could be that the Dawn and Dusk runes can't defeat the Sun Rune individually, but used together may be able to overcome the true rune's power. The two might be halves of a yet-unmentioned true rune in the game, since the other two true runes in the game are still speculation. Regardless, I'm guessing we won't know much more about the runes or the story behind the game until it's released in Japan and we gain info from people playing it, and even that's only giving us a precious few weeks before its release here.
As for me... I like a little info, but I don't want to spoil the whole story for me. I'm happy with what I already know, and am willing to wait a month and a half to satisfy my curiosity.
Just my lengthy two cents.