Broken Base: Some find this game a step down due to the simpler storyline and setting in comparison to Diabolical Box and Unwound Future while others like it because the storyline is much simpler and some don't care either way.
Fridge Brilliance: Remember when Luke was saying that the specter was controlling his dad? Turns out, the operator of the specter was.
Crosses with Foreshadowing: at one point, Beth laments that Doland's handwriting has deteriorated since Clark became mayor. This makes a lot more sense when you realise that this would be around the time that he was taken hostage and replaced by Descole, who probably wouldn't have bothered with copying Doland's writing style.
When you think about it, Loosha most likely IS the specter from the legends - That is, she is called to save the town from it's darkest moments, and responds to the song of a flute. Therefore, the legends are true, with the added fact that she's also defending the town from Descole's machines - which are the pack of "Bandits" from the story!
Hype Backlash: After the original hype for the game died down, many people began to see flaws in the game, particularly its storyline. Many considered it dumbed down after the intensity of Unwound Future. This is perhaps not an entirely invalid complaint, considering the game begins with the promise of a giant monster destroying a town, the town itself being cold-hearted and monstrous under the surface (considering they're glad that Arianna's father committed suicide and that they've supposedly ostracized a dying child because they consider her a witch), orphaned and criminal-minded street children trying to make cash after the town's industry collapsed, and not forgetting that said industry was closed down because it was polluting the village's air and gave Arianna what is implied to be lung cancer. This is neatly and jarringly cleaned up after the introduction of Loosha, a giant loving blue manatee, and the power of the Golden Garden even curing Arianna of her deadly disease. It's even revealed that her father's death was simply an accident. Conversely, many fans welcome the return to a more simple storyline along the lines of Curious Village, but even many of those on that side of the fandom agree that Loosha's introduction is more than a little out of left field.
Sidetracked by the Gold Saucer: The Specter's Flute contains an unlockable extra (available after finishing the game) called "London Life": An entire simulation RPG (in the vein of Animal Crossing or Harvest Moon) set in the Laytonverse. It's not so much "receive a cool extra after finishing a Professor Layton game" as it is "A couple hours of the usual Layton rigmarole serve as a Brain Gate for a really cool Layton RPG." In the North American release, you can play it right from the start, so you can really get sidetracked from even the main story. Europeans can't get sidetracked since they won't get it.
Toy Ship: Luke has shades of this for Arianna who might also have the same thoughts. And then there's Sean, but his is completely one-sided to Arianna.
From London Life:
Goddamned Bats: Which drain your Happiness when you run into them.
They can also appear in swarms on some days, even during the day!
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