All I can personally say on this front is that my decision to rank Ptolus 6th in Best D20 had very little to do with Ptolus and a great deal to do with the quality of the other products on the list.
I considered Helios Rising to be a better setting book that Ptolus because I felt it was more creative and innovative and also because it asked and answered questions about the setting it described that I was more interested in than the questions Ptolus answered.
Similarly, I found that Warlords of the Accordlands gave me a sharper and more complete picture of a setting than Ptolus did. Instead of the cosmology/mythology having one cool/interesting aspect, as did Ptolus did, I found that Warlords offered many. I also found that the adventures and adventure hooks provided in Warlords were less railroady than Ptolus was. (Not that I consider Ptolus to be a big offender in that area; it's just that Warlords was even less so). Also, and this is a matter of personal taste, a lot off Ptolus's schtick is the routinization of magic and the way that people have adapted it into their everyday consciousness. I find such a world less exciting than a place like the Accordlands where it seems like people are most interested in striving for magic that is beyond their reach. The insufficiency of magic seems like a more engaging (for me) theme for making magic commonplace.
Five Fingers, interestingly, was there, at least in part, because of its brevity. It wasn't just that people felt like they had a feel for the setting when they closed the book. They had it immediately, within the first few pages. When I was reading the book, I was reminded of Italo Calvino's great book Invisible Cities in which the author is able to convey the whole idea of a fantastic city in the space of a page and a half. I think, also that the idea of a place's history being essentially written into the physical landscape itself was a powerful one.
Ultimate Power, on the other hand, was a completely different kettle of fish. As one judge put it, the book "completes" Mutants and Masterminds, giving GMs and players much-needed flexibility to design almost any set of powers. Instead of souping-up hero powers, this book had the courage to offer nothing to those seeking to get more powerful by buying more books and, instead, focused their volume on empowering GMs and players to convert basically any super-powered character from film, novels or comic books into M&M terms.
Etberpunk: Upload was very close, in the running to the other Scope book for this setting that Goodman released. It was almost a toss of a coin as to whether Etherpunk or Mysteries of the Occult was the better of the two. I loved both books and felt that they, together, filled-out the Etherscope universe in terms both of fluff and crunch.
I felt that all five of our selections were, in one way or another, more innovative than Ptolus, more important in completing their product line than Ptolus or were simply better settings than Ptolus was.
As for why Ptolus made Product of the Year and some of these works did not, let me offer a few general comments about the judging process that may be helpful:
(a) sometimes, when a couple of products are neck-and-neck for 5th place in a category and we end up awarding one an honourable mention instead of a finalist, the next time that happens to the very same product, we often favour the one that narrowly lost the last time we were forced to almost toss a coin to see which one won.
(b) late in the selection process, as time for negotiated consensus runs down, we sometimes have to fall to majority voting to see which product wins. Because we couldn't reach consensus on every category, some categories are more characteristic of majority rule and others of a consensus amongst all the judges.
(c) in any voting system, no matter how fair, the length of a list matters a lot. This is even true when negotiating a consensus. Lists of 10/12 products look a lot different than lists of 5/6 products and have very different properties. Being the seventh-best or ninth-best in a judge's mind matters a lot in the Product of the Year category whereas it is irrelevant in the other categories we judge.
I hope that this answers your question.