I just got to beat the big bad of spirit tracks and I actually enjoyed the fight. It was one of the most difficult fights in the entire game. Not that it took a lot of lifepoints, but it did drain my battery once. But it was still totally awesome.
Still the difficulty level is not that high. Any experienced Zelda player can finish this game in record time.
I do have some suspicions about certain characters although the story never confirms or denies those suspicions.
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Anjean is actually Tetra. Anjean has a striking resemblance to her. Not only in looks, but also in attitude and behavior. She has that cocky and free spirited vibe around her.
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Malladus look when merged with Cole, is really like that of Ganon (the pig form). Demon King and great evil, could thus be a form of Ganon. (Although I don't really like that thought)