While this status to the Legendary Pokémon of the films is to be expected, Latias takes special mention for being rather fondly remembered by most people who saw the movie, thanks to a combination of her personality, the fair amount of InterspeciesShip Tease she has with Ash, and becoming a woobie over the course of the movie.
Though to a lesser extent, Annie and Oakley have their share of fans for their competence, choices of Pokémon (Espeon and Ariados), acrobatics skills, technology and designs.
Evil Is Sexy: Annie and Oakley, with their midriff-baring black leather outfits and slim, curvaceous, well endowed figures.
Fanfic Fuel: Alto Mare is a pretty popular choice of places used in fanfics. Being based on Venice no doubt helps its cause.
Harsher in Hindsight: My Best Friends being the film's end credits song, considering this was the final film with the original cast.
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 his or her 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.