I strongly doubt that Skyward Sword will be that similar at all to Majora's Mask. Though Skyloft may be larger than the usual cities in Zelda games, perhaps larger than Twilight Princess Castle Town and more on the scale of Clock Town, I do not believe that it will be nearly as much of a hub for story and gameplay, namely geography, as Clock Town was.
Majora's Mask was probably the least exploration based Zelda game. This is because the overworld was relatively small and easy to navigate, basically as easy as seeing the familiar red balloon and having a few rupees. Skyword Sword, on the other hand, seems extremely exploration centric, probably the most since Legend of Zelda. Considering that we will have three different world, two full, one more like the Dark World (this is more than any Zelda game ever, several had two worlds with slight variations such as Ocarina of Time and A Link to the Past, but Skyward Sword will have the Sky, Hyrule, and the Siren World, the Siren World being the partial one), exploration seems to be a key factor. Also, factor in the knowledge that many field areas will be dungeon-esque.
Though Skyloft will doubtlessly have many characters, I doubt that they will be as much of a central part of the gameplay as in Majora's Mask. It almost felt like, with Majora's Mask, you couldn't really get the full experience without doing all the sidequests and helping the characters. I'm almost certain that Skyword Sword will feel very full just from the exploration and dungeons.