My favorite movie is probably Pokemon 2000, but I know that's in part because I'm a huge sucker for the Johto games and Lugia's one of my favorite legendaries.
I also really like Pokemon Heroes; though it has nothing to do with the plot, villains or even the bestiality.
I loved the setting, Latias is one of my favorite Pokemon of all (not a pokefucker, though) and the scene - or more specifically the music - that plays when Ash is chasing human!Latias around. That score alone makes the movie worth a watch for me.
https://www.youtube.com/watch?v=MT2EiDnQfIM 
