I enjoyed Apollo's Song, but there are definite weak points (which seem to be focussed at the beginning). I felt the prologue was heavy-handed, so it just didn't grab me as much as it should have, and I didn't care for the WWII chapter either. This far in to the book I still knew very little about the characters, so had formed no real attachment to them, and out of all the storylines this spent the least amount of time introducing them or portraying their interaction. Again, it just failed to grab me and draw me in to the story.
However, reading further the story arcs got longer and more interesting, and I found the rest of the book fascinating. The Queen Sigma storyline in particular had some very moving scenes. By the end I was thoroughly involved with the characters, and even willing to admit that perhaps I shouldn't have written off the opening chapters so lightly.
It's an interesting point that this could have fit in the Phoenix series, as I can easily imagine the Phoenix in that role. I think I prefer it as a stand-alone work though, because this way the goddess can be a bit more ambiguous. I think of the Phoenix as acting cruelly in some instances, but doing so with some notion of objectivity backing her up. With the goddess, I like the fact that there's an undercurrent of personal hatred behind her actions, along with the main concept of fate.
(Also, I can't think of a better choice for lead actress than Melmo, given the themes of Apollo's Song and the sex-ed nature of her original role!)