In the newest issue of UK's Official Nintendo Magazine, Eiji Aonuma, in an interview, states that Skyward Sword takes place before the betrothed Ocarina of Time. Since Majora's Mask is a direct sequel to Ocarina, then Skyward Sword cannot be a Majora's Mask sequel.
Take from GoNintendo:
“Yes there is a master timeline but its confidential document! The only people to have access to that document are myself, Mr. Miyamoto and the director of the title. We cant share it with anyone else! I have already talked to Mr. Miyamoto about this so I am comfortable in releasing this information – this title [Skyward Sword] takes place before Ocarina of Time. if I said that a certain title was ‘the first Zelda game’, then that means that we cant ever make a title that takes place before that! So for us to add titles to the series, we have to have a way of putting the titles before or after each other.” - Eiji Aonuma
Well, shit. If Skyward Sword is before OoT, and most put OoT at the beginning of the timeline, could Skyward Sword actually bring into view another conflict? OoT took place immediately after the Hyrulian Civil War (which Link's mother escaped into the Kokiri Forest from) and the Imprisoning War takes place in the 7 years that Link was in the Sacred Realm. The Imprisoning War was talked about during ALttP, while the Hyrulian Civil War was created for OoT (the Deku Tree Sprout told Link about it after you beat the Forest Temple), then SS might even bring into light a new conflict.
For even juicier tidbits, a while back, it was stated that Skyward Sword actually shows the creation of the Master Sword, which was originally known as the, you gottit, the Skyward Sword (which transforms into the thing you see in the original artwork). Taking that plus the "SS is before OoT," then we've got ourselves one hell of a Zelda title coming.