These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Fan-Preferred Couple: Darkrai/Alice since the former risked his life to save the latter multiple times, while the latter felt worried whenever the former was hurt. You'd be surprised to see how many fans ship them instead of the Official Couple Tonio/Alice.
Genius Bonus: The Oración piece drawn at the back of the photograph of Gody and Alice on a bench, if played in the treble clef, is the same as the Oración actually played during the movie, albeit only the melody line.
Iron Woobie: Darkrai, who never meant any harm, was cared for by Alicia, and went on to eventually save Alice's life, was still oppressed and antagonized by the people of Alamos Town.
Just Here for Godzilla: Most people only watched this movie to see the ongoing battle between Palkia and Dialga and/or see Darkrai.
A few just wanted to watch the beginning of the movie with all the past generations of legendary pokemon battling in one scene.
A nightmare within a nightmare: when Ash was put to sleep by Darkrai's Dark Void, he sees a really menacing projection of Palkia.
Watching Alamos Town slowly disappear into another dimension by Palkia.
Paranoia Fuel: You see the vast fog over your town? That's no ordinary fog. Behind that fog isn't clear blue skies, but a whole different dimension that some invisible being has sent you in. Oh, and by the way? Your loved ones who are asleep will never wake up and are suffering from never ending nightmares.
Tear Jerker: When Ash and gang cry over Darkrai's "death" at the end.