Sorry for the late response. I was having trouble getting on the site without a computer. I was trying to access via my wii, but it didn't work.
Anyway, behind the story, is that people that wouldn't normally "exist" in Hyrule have been mysteriously appearing; likewise, the same is occurring in Tellius. Monsters are invading the native lands of Tellius and soldiers (both beorc and laguz) are experiencing mistreatment from majority of Hyruleans, monsters included.
What caused this phenomenon is unknown, so a small, preferred group of travelers from both Hyrule and Tellius would eventually come together to figure out the source of the problem. However, both sides wouldn't officially start off together, since both lands are experiencing strange occurrences. In fact, I'd want a separate group of beorc and laguz from Tellius to group together then a small group of maybe monsters and hylians (or whatever species the user(s) themeselves would like to be, like an Imp Poe or a Twili) and group together.
It's okay; the only thing from Skyward Sword is the background story and that Skyloft is in the role-play. Other than that, no other elements of the game are in there.
Link to the Past, TP, Minish Cap and Fourswords Adventure are my favorite Zelda titles. Ocarina of Time would be a favorite if I didn't get scared at the Shadow Temple. XD