Broken Base: The dub-edit where Ash mentions a "good friend" (obviously Misty) who left him and who he misses every day when talking to Max. Some (especially Pokéshippers) like it for the continuity it creates and find it to be rather sweet on Ash's part, while others dislike it for being another example of 4Kids altering the original in an attempt to push Pokéshipping.
Hilarious in Hindsight: Take a good, long look at the fake Groudon from this movie. Flash forward to 2014 and the Gen IIIremakes, Omega Ruby/Alpha Sapphire, introduce Primal Reversion, a transformation for the mascot Legendaries similar in function to Mega Evolution. Three guesses what Primal Groudon greatly resembles.
On that note, the final enemy of season 19 (XY and Z) is very similar to the fake Groudon in this movie: a gigantic implacable imposter of a legendary ground type Pokemon, seeking a shiny source of power.
They Wasted a Perfectly Good Plot: That subplot with May's wishing thing? Yeah, it seems like something important is going to come from that, but then she forgets to put in the last piece.What an Idiot!! In May's defense, though, they reached Farina by the time of the last night, and she got preoccupied with everything that was going on at the time.