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.
Fanon Discontinuity: Kanto/Orange Islands Fans (and Pokeshippers) fed up with the long-running Pokemon series never ending or having any big dramatic shake-up beyond cast changes look to this movie as the grand finale. Amongst boxes ticked are Ash fulfilling a prophecy, working with the legendary birds, saving the whole world in the process (which would in a logical world, make him a Pokemon Master), and Misty more or less putting her foot down and vowing that Ash will "always have her".
Memetic Mutation: This is the movie where the meme that Ash is The Chosen One for everything started. The prophecy springboarded the tendency. It perpetuated to the point that a common fanfiction cliche is for Ash, being The Chosen One, would get amazing powers on top of commanding numerous legendary Pokemon.
Ship Tease: There is a very obvious reason as to why Pokeshippers love this movie.
Melody also makes it quite clear she has a thing for Ash.
What an Idiot: Lawrence III apparently doesn't realise that he's behind the catastrophic weather patterns, despite the disruption he's caused being the only logical conclusion. He also absurdly decides to let the main characters, who're clearly angry at him, loose in his gallery with the imprisoned Birds. When you tool around in an airship the size of a community college, you couldn't think of any other place to put them?
The part specifically citing Ash as the Chosen One, and thus the Prophecy Twist, was a Dub invention. Originally, the prophecy only cited that "an exceptional trainer" was capable of averting the catastrophe.
Also, Lawrence III's reference to his collection starting with an Ancient Mew Card was added into the dub. That information, in the original release, was not stated in the film itself: Rather, it was stated in an information pamphlet that also revealed that Lawrence III was an orphan, and the name of that airship of his. As you might guess, this pamphlet was Japanese only, and since the card appears near the end of the film, it had to be mentioned somewhere in the English version.