My Best Friends being the film's end credits song, considering this was the final film with the original cast. It doesn't help that it caps off a medley with the prior song being The Time Has Come, which first played during Pokémon S1E39 "Pikachu's Goodbye"' and ends its section with "Somehow, someway, we'd have to say goodbye."
It Was His Sled: Latios dies saving Alto Mare at the end. A lot of fan art of the two Eon Dragons gives this away.
Moe: Latias: in her human disguise she's a bonafide Mysterious Waif, and in her true form she's a cheerful, affectionate Genki Girl of a Pokémon. She racks up multiple Woobie points along the course of the movie for good measure.
The zombie fossil Pokémon; blank-eyed Super Persistent Predators that, according to the dub at least, belonged to an evil Trainer in life and attacked innocent people at their command. The sight of Aerodactyl stalking Ash from a distance as he's paddling a gondola in particularly creepy, and Kabutops came frighteningly close to skewering him on one of its scythe blades.
The tidal wave; large enough to engulf the whole city and with enough force to shatter solid stone, as shown by an abandoned cathedral that happened to be in its path.