I voted the first movie on this a while back.
I guess that I am just a big fan for Mewtwo's character, being made as a weapon, but destroying his creators as he refuses to be their tool, and tries to do what he thinks is right based on his anger. I still cry every time I watch the part where pikachu tries to revive Ash. Apart from those the pokemon in the movie tend to come off as epic, the battle in the opening credits, introducing the other champions pokemon, and when the clones show how strong they are.
Of course their is always nostalgia being a part of it, I do think I enjoyed the setting more in the second movie.
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Through dream I travel, at lantern's call
To consume the flames of a kingdom's fall