There is an interesting wrinkle that it can be hard to split certain stories.
I think Superior Spider-Man will make the list, but would be it be a shorter arc (IE- the first three issues by Slott & Stegman)? Will it be the entire 31 issue mega-arc? Will it be the 31 issues of Superior Spider-Man, and three-part "Dying Wish"? Are they going to figure out another way to qualify a group of issues? My suggestion would be to group the first nine issues with the Ghost Peter plot as one story for these purposes.
Likewise "My Dinner with Jonah" occurs during a 17 issue storyline by Zdarsky.
Nick Spencer & Ryan Ottley's first issue is "Back to Basics Part One." But the rest of the arc covers a different storyline (Peter & Spider-Man split into different personalities.) Is it okay to just consider the first issue, which did get really good reviews, as one story like "Spider-Man No More" isn't necessarily seen as part of a larger arc introducing the Kingpin?