The two can be viewed similarly for a few minute reasons, but other than that, the two are almost like polar opposites. Skyward Sword was a very straightforward game that shifts the player's attention away from sidequests, while the core of Majora's Mask lied within interacting with characters and completing the seemingly endless amount of different sidequests with the three day cycle.
Most gamers would like to think of SS as a very upbeat game with a lighter tone than most Zelda games. The Wind Waker would probably be unanimously thought of as the brightest Zelda game, but Skyward Sword comes as a close second. This is mainly because cool colors are used to a minimum, and if they are used, they are always very bright. For the most part, environments and characters in the game consist of warm colors and don't have tremendous amounts of detail. This is a product of the impressionist art style that makes the game looks like a watercolor painting come to life.
On the other hand, Majora's Mask is arguably the darkest Zelda title to date. The looming threat of the Moon becomes greater with each passing day, bringing the destruction of Termina ever closer. While Clock Town seems to go about its business as usual, Link is able to get an inside look at the panic surging through the townspeople in the mayor's office. Only guards are courageous enough to remain on duty, and characters often comment about the horrific-looking Moon that dangles above them. More importantly, this impending sense of doom makes Link constantly feel rushed to complete sidequests.
It is ultimately up to the player whether or not to help out those in need before their final moments. Anju and Kafei's quest for love is cut short by Majora's antics, and Link can decide to get involved or do nothing about it. What the player will find is a tale of anguish and a bond between two lovers that can't be broken, no matter how Kafei appears. In the end, the two embrace in the final seconds before the Moon crashes into Termina - a chilling scene that amplifies the dark atmosphere of Majora's Mask. The sidequests capture the dire situation of the people in Termina, and MM brings an element to the table that was never seen before in a Zelda game: death.
Both are extraordinary and are generally considered underrated, which might be one of the similarities between the two. However, the two seem to be on opposite ends of the spectrum in several ways. Majora's Mask's gameplay is very complex while Skyward Sword's is simplified. MM veers from the beaten path and approaches Zelda in a much more emotional and fragile way, while SS continues the franchise's tradition of epic adventuring.
Perhaps the only real similarity between Majora's Mask and Skyward Sword is that the titles of both games are examples of alliteration.