Also Rebecca due to being a Meganekko with a Metagross and Tyrannitar (seen in a later movie), making her one of the few anime characters with more than one pseudo-legendary.
Franchise Original Sin: This was one of the first movies to have an antagonist legendary Pokémon who was a Non-Malicious Monster working on its own accord, with the conflict coming from a misunderstanding rather than the purple-crystal Deoxys actually being evil. While relatively new for the films at the time, many have accused later movies of doing that exact pair of tropes over and over again to the point of annoyance.
Harsher in Hindsight: Ash's last line in the English dub of the movie ("Hey Pikachu, I'm glad that you and I will always have each other.") becomes this to fans of the 4Kids dub after the entire English cast, including Ash's own voice actor, fan-favorite Veronica Taylor, was replaced by new voice actors in 2006, the year after this movie was released in the U.S.
It also serves as vague but clever Foreshadowing of the next movie, where that very line would be tested (and where the 4Kids voice actors would be playing their roles for the last time in a Pokémon movie).
The green-crystal Deoxys was reduced to a crystal and had to regenerate its body; a very similar concept to the Gems.
Just Here for Godzilla: There is a group of people who only watch this movie because Rayquaza and/or Deoxys is in it.
Special Effects Failure: Plenty of the CG has not aged well, and it's especially obvious with the two main legendaries. There's a reason why there's less CG in later Pokemon movies.
Tough Act to Follow: The film is one of the more fluidly animated and well paced Pokemon movies, and sports an overall entertaining experience throughout. While it doesn't hold up as well as Mewtwo or Entei's films, but is still thankfully amongst the best.
The Woobie: You kinda have to pity Tory for having a phobia of Pokémon in a world utterly obsessed with them.