This movie is what Pokémon 2000 was originally slated to be.
The original rumors surrounding movie 2 were that the villain was a mad scientist out to intentionally destroy the world. In the finished product, he's only a slightly addled art collector... but then a production sketch surfaced that claimed he's also a scientific genius, something that never manifested in the movie. Were the rumors true? Movie 11's Big Bad is, you guessed it, a mad scientist out to intentionally destroy the world (eventually). Both characters also have huge airships and are kept company only by their feminine-voiced computers. The Reverse World is actually the afterlife in the Pokemon world.
Think about the fact that in the game the only way to get into the Distortion World post game is through Sendoff Springs which said to be where the deceased to go journey to the other side. It should also be noted that there are several building in the Reverse World, but not once are any of these buildings entered even though it would seem that they could be. This is because they are actually inhabited by the souls of the deceased and one of the reasons Giratina is there is to keep them in line. This may also be one of the reasons why Giratina isn't so fond of living people being in the Reverse World.- Also the only way for Giratina to travel between the Reverse World and the Real World is through mirrors and other reflective surfaces. Mirrors are commonly portrayed as portals to the afterlife.
- This explains the random green lights in the Reverse World. They're portals to the underworld.
The Creation Trio aren't pokemon.
It's been established that all pokemon share a common language, yet no one aside from possibly Arceus seems to be able to understand Palkia's, Dialga's, and Giratina's vocalizations. The plot should have been resolved the first time Ash's group went into the Reverse World, where Giratina could explain to Shaymin what it wanted from it, but no one at any point makes an attempt to ask it why it's targeting Shaymin or tries to translate its shrieks. Throughout the movie, Giratina clearly is talking, but the pokemon react the same way to its shrieks as the humans do. It still uses pokemon moves and aligns with the typing system, though; so, going off of that, it's possible that the Creation Trio aren't themselves pokemon, but rather the prototypes for the creatures that Arceus made later when it had a better handle on what it was doing.