Setting aside the pokeshipping aspect of M02, which is your favorite Pokefilm?
The first one. A little bit of it is probably nostalgia (it’s the one Pokémon thing that genuinely makes me feel nostalgic, not even other parts of the OS have that effect), but aside from that, Mewtwo’s story is genuinely one of my absolute favorite plots to come out of the Pokémon anime (especially if we count the “Birth of Mewtwo” prologue, which was unfortunately left out of most Western releases…).
The second one is a very close second though, even not counting the pokeshipping. Of all the movies (that I’ve seen, still missing the XY ones and the 20th) it’s the one that feels… the most grand? I’m not sure how to explain it exactly. I can actually believe that the world is in danger and feel the situation Ash finds himself in, while other movies, even when they feature events potentially just as catastrophic, lack something that makes things feel quite as big-scale.
(Honorable mention to the Lucario movie.)