Air Jousting: Apparently, when Palkia's pearl is damaged, high-force collisions cause damage to space in general. Guess what makes up half of Dialga and Palkia's combat.
All There in the Script: The three coordinators who each have one of Sinnoh's fully evolved starter pokemon. Although they weren't referred to by name in the dub, Pokémon.com has since released their names as Kai, Allegra, and Maury.
Androcles' Lion: Why Darkrai was loyal to Alicia and Alice, because of the former's kindness towards him.
Attack Hello: Before Palkia even knows he is there, Dialga fires with Draco Meteor, flies in, and tackles Palkia straight to the ground the second time they meet.
Avoid the Dreaded G Rating: This movie is the very first Pokemon movie to ever be rated PG in the United States even though some of the earlier Pokemon movies had their own share of disturbing factors yet were still rated-G.
Dreaming of Things to Come: Ash's nightmare reveals the presence of Palkia in Alamos Town. In the past, Godey dreamed of the future, catastrophic battle between Palkia and Dialga and built the Space-Time Towers before said event.
Gilligan Cut: After finding out Palkia was behind the strange occurrences happening around town, we have this:
Dawn:But that means Palkia is here!
Brock:But where is that?
(cuts to Darkrai)
Glowing Eyes of Doom: The Time-Space Duo's red eyes turn orange and glow when using their powers. Especially noticeable during their first battle in the beginning. Darkrai also does this at the very end.
Hope Spot: As Dialga uses Roar of Time and Palkia uses Spacial Rend, Darkrai gets in the middle of them and surrounds itself with a shadow orb to take the hits. The orb surrounds all three of the legendary Pokémon and traps them inside for the time being. Just when you thought Darkrai would be able to hold them off, both dragons break free and fire at the defenseless Pitch-Black Pokémon, killing him.
Left Hanging: It was never explained why Dialga and Palkia are fighting in the first place, until the 12th movie reveals that it was because Arceus was awakening that the domains of time and space are overlapping.
Light Is Not Good: Both Dialga and Palkia are actually given villainous roles in the film.
Never Trust a Title: The English title would have you believe that Darkrai is the villain of the movie. Turns out it just wanted to stop Dialga and Palkia destroying Alamos Town, despite the fact that everyone thought it was evil. Obviously the Japanese title subverts this.
Nigh-Invulnerability: Besides Palkia's shoulder injury, the Time-Space Duo don't seem to receive a single scratch from their heavy attacks against each another, and neither of them seem the least bit fatigued during their ongoing battle. Heck, even Palkia's wounded shoulder, which is implied to be one of its lungs, doesn't seem to hinder its battle against Dialga. Maybe Justified for Dialga since he does seem to be Made Of Diamond.
No Endor Holocaust: Nearly all of Alamos Town had been either destroyed or disintegrated by the Time-Space Duo, yet there is no mention of death and those who had been shown to have died end up coming back.
Non-Malicious Monster: Palkia and Dialga. Both thought the other was threatening its home and instinctively attacked. Alamos Town was dragged into the picture when Palkia escaped and hid there in order to hide itself from Dialga. Once found, they continued to fight, oblivious to the destruction around them.
Spoiled Sweet: Alice. Just because she is gorgeous, rich, and owns a large garden, that doesn't stop her from being one of the nicest and most loyal of characters. Her grandmother counts, too, since she allowed Darkrai to stay and enjoy her garden.
Super-Persistent Predator: Dialga is this towards Palkia. When the latter left their first battle due to an injury, Dialga was outraged and searched across dimensions to find and finish off his rival.
Taking the Bullet: Darkrai in the climactic battle. He spends roughly half the fight doing this.
Watching the Sunset: The ending. Everyone watches the sunset once Alamos Town is back in shape, the Dragon Duo ended their fighting, and Darkrai is alive again. Also, Tonio and Alice are finally together.
The Worf Barrage: Darkrai, who has been shown to beat a whole crowd of Pokemon with just one of his attacks, can barely mark a scratch on neither Palkia nor Dialga.
The Worf Effect/Make Way For The New Villains: Palkia and Dialga do this to the Unown to establish how powerful they are. Back in the third Pokemon movie, the Unown were seen as powerful, reality warpingabominations who can make the wishes of a little girl come to life. Here they are running for their lives away from the two dragons fighting in their dimension.