Having finished Sudden Death, which I hadn't read before, my ranking for SS Arc Qualifying Rounds stories is:
I'm absolutely willing to admit I'm biased for fine but I know even many fine fans don't like Sanctuary, or least didn't when it originally released. But I genuinely like the story, what it told about Wataru, how Tomoya has hell of a mental strength, Tori's anguish he's trying to set aside... and of course Eichi swooping in, being the one who knows how to wake Wataru up, and then hissing at Tomoya in jealousy because he's afraid he'll lose Wataru. It also shows a lot of what's going in the background because Nazuna is most of the time in the Gatekeeper's office.
And Sandstorm I have to rank second because of how much I've been thinking about it. I really liked how Kaoru was written in it and 2wink's "did they do it maliciously or had they altruistic motives and who did they do it for" thingy was really interesting. Also, muting Rei was a good idea (and this is silly thing to say for a fully voiced story as someone who likes Toshiki Masuda a lot, especially as Rei. ;P) because like they noted in the story, when both Rei and Kaoru were unavailable, Adonis had to step up.
Secret Service is the most lore-heavy and I adore it. It could very well be in the second place too. Also liked the "who's on whose side" and content for the both units involved. And oh the scene where Hiyori goes "I don't know what's going on and I don't care, I'm here just to save Nagisa!" and almost jumps from the temple roof when he finally sees him.
In Satellite I liked how we see how Tatsumi can reason himself to do things that can hurt someone while helping someone else. Obbligato later explores his way of thinking more but Satellite was a great glimpse to it too. Also, Trickstar in the jungle were hilarious.
Submarine had a similar situation with Keito and Souma as Rei and Adonis in Sandstorm which I liked. Souma is ok with being "a follower" and being lead (not in a bad sense, just that someone else is thinking the big things and making decisions) but it was good to show him that he is capable and also that he *is* ok with Keito in the lead. Bonus for the seasick Kuro (sorry Kuro...).
Shinsekai I don't have that many thoughts for. Some background shenanigans were interesting, but mostly that's one of the stories I point out when talking about similarities between Natsume and Eichi. How Natsume wants to control people and situations but because he doesn't have the money and power, he can't. Until this VR thing. And of course there's the iconic "can I call you darling?" for Mika and Shu, for that alone the story can't be the last.
Sudden Death was maybe the only one I was disappointed with. It had good moments, like Leo thanking Kohaku for saving Madara, funny stuff with Leo and Izumi, and the glimpse into Tsukasa and Kohaku's childhood was interesting. But otherwise it felt like Knights waffled on about same thing for endlessly and Crazy:B had nothing to do. Not everyone had big roles in all the stories of course but Niki and HiMERU particularly felt only decorative in this.
Now waiting for the Finals!!! EEEEEEEEP!!!