The Legend of Zelda: Spirit Tracks/WMG

The villain is still Hijacked By Ganon
Consider Malladus' true form: a floating, gaseous head. Who else have we seen look like this? Ganondorf (in Twilight Princess). Other elements (the Ganontrain, the fact that Cole-Malladus is basically Beast Ganon with a mustache) lead me to think that if Ganon isn't masquerading as Malladus, he's the one who gave him the power to free himself, and couldn't resist putting his appearance on his underling's body and weapons.
 * As the Wind Waker/Phantom Hourglass character Niko appears in this game and Tetra is stated to be a friend of Anjean's, wouldn't that mean that Ganon is doing it while his head is still impaled by the Master Sword?
 * Alternately,

Cole is a reincarnation of / is the Happy Mask Salesman.
There's just something very.... Mask Salesman-ish about Cole, and it's not just the hair; it probably has to do with the insanely twisted expressions they both pull off, and the themes utilizing Psycho Strings that are related to them. Then there's the inexplicable creepiness involved with the Mask Salesman that was never fully explained.

Zunari was from the Snow Realm
In Wind Waker, he mentions traveling across a cursed sea from a land of blizzards; since it's likely that Malladus was still causing havoc around that time, it's not unthinkable that the entire Snow Realm would be stormy (like the path to the Snow Temple the first time through) and the Ocean Realm/the borders of New-Hyrule-to-be would be harsh enough to call "cursed". He might even be one of the original inhabitants, since one of the Anouki outright states that they aren't locals. Failing that, he might actually be from Anouki Island, since his statue says that he came from a "C-c-cold Island". (This could be an assumption, though, since the description came from the sculptor who, like everyone else on the Great Sea, can't fathom the idea of a mainland.)

Spirit Tracks' Link is Minish Cap's "Hero of Men"
I'll admit, I'm not very good at working out timeline issues, but it kind of makes sense for MC to come after ST-- mostly land-wise. Hyrule never seems to stay peaceful for very long, so it's possible that he wound up going on another adventure-- possibly with Zelda in tow-- that had to do with the Minish/Picori; Light-force-wise, the legends could simply be incorrect (like we haven't heard that a million times) and assumed that  received the light-force from the Picori, since nobody but Link and Zelda actually know what happened with the Spirit Tracks and couldn't know that   had already used it on one occasion. Aside from that, there's not too much proof-- the 'Antiquiated shield' (which ST Link is presumably in posession of) appears in one of the stained glass windows in MC's opening, but that doesn't necessarily help the argument.
 * Jossed by Hyrule Historia. According to the official timeline, Minish Cap comes right after Skyward Sword at the beginning of the timeline, while Spirit Tracks is (for now) at the very end of the "Adult" timeline.

Spirit Tracks is the latest/"most recent" adventure
Same temporally-ignorant troper as the above; alternate to that theory, none of the other games come after Spirit Tracks (as of yet). There are already trains and train tracks-- who's to say that technology won't march on in that timeline? It doesn't make sense to go from having trains and steamboats to getting around the entire kingdom on foot and using rafts. Maybe there won't be anything added to that timeline, or maybe we'll see a Steampunk installment or a literal Urban Legend of Zelda, eventually. (Doubtful, but hey, this is WMG).
 * It is not stated, but it is possible that with Malladus' defeat, the Spirit Tracks (which worked as his chains) will vanish, leaving the people of New Hyrule to either scramble to figure out how to cast railroad tracks, or causes the trains to become lost knowledge. For all we know, the trains could have been used by the native people of the land - before Tetra and her crew founded the kingdom.
 * One of the endings features Link going ahead and becoming an engineer, though, and that's after Malladus's defeat. So, in that ending at least, the tracks were still there...

Upon moving to New Hyrule, Aryll lived in Papuchia Village
It's in the Ocean Realm right on the water (easy to adapt to after growing up on an island), is a fishing village relatively close to the Forest Realm/civilization and there are birds swarming the place. It's like New Hyrule's version of Outset (ignoring the PAL name for Aboda).