The first thing I thought when I saw this new dude........where have I seen that pattern on his legs before? Luckily, I just happened to be playing through
MM at the time, and so when I pulled out my sword it hit me. Initial, thoughtless reaction: HOLY CRAP ITS MAJORA! Then I calmed down.
Seems like an attempt to link
MM with the rest of the timeline. Remember, the Mask was not necessarily a Terminian creation, as it was taken there by the skull kid who stole it in Hyrule's lost woods. The teleportation may link this new race to the Twili, and perhaps be the dark interlopers themselves.
Here's my take on it:
This new race is the race the interlopers came from, therefore it was only a portion of the race that were banished to the twilight realm. As outlandish as it sounds, I believe that this new tribe will eventually become either the Shiekah, the Gerudo, or both (note Midna's Gerudo orange hair and Shiekah red eyes).
As for skyloft, probably just a one off place that we never see again after this game.