The plot is an alternate universe version of The Legend of Zelda: Link's Awakening. This is why Oshus and Bellum seem so similar to the Wind Fish and DethI respectively. It even explains the whole All Just a Dream ending.
Tetra being sought out and drained of her life energy by the Ghost Ship makes a lot of sense when you consider the events of The Minish Cap, wherein you learned that the princesses of Hyrule have the power of the mythic Light Force flowing through their veins. Furthermore, Spirit Tracks and Skyward Sword have since revealed that Tetra is also the inheritor of a wealth of sacred spirit power as well as that of the ancient goddess Hylia. Is it any wonder that Bellum was so intent on recapturing her, with these things in mind?
The way that one would get the crest for the Sun Keynote Pressing the 2 screens together is brilliant because many players might get frustrated and close their DS to look up the answer, thus solving the puzzle.
Which is also carried over into the Virtual Console port for the Wii U, in which "open and close the menu" substitutes for "close and then open the DS" - many players, upon being stumped by this puzzle, would open the menu to go onto Miiverse and ask for help...only to return to the game and discover that they solved the puzzle without knowing it.
In the Goron Temple, Link joins fates with Gongoron, who spells it out that this means one of them will keel over in the event that the other does, so both party members are well aware of this during this part of the game. If this happens, the character you are not controlling can be seen dying just after the one in play dies. Just imagine their reaction when they see their partner fall in battle.
