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- When the timeline is rewritten, it is not stated completely that Arceus fell into a sleep that lasted until the present. We see three of its Plates in a flashback in Pokémon: Hoopa and the Clash of Ages, indicating that it helped create the Prison Bottle. This could signal that if the Jewel of Life was never returned, Hoopa would still be terrorizing Dahara City.*
- Why is Pikachu, of all things, able to harm Arceus when the Creation trio can't? For starters, the trio only landed attacks that could be negated somehow (Hyper Beam and Aura Sphere were negated by Arceus turning into a Ghost type, while Giratina's Will-o-Wisp was negated by the Flame Plate since Fire types can't be burned), possibly for fear of collateral damage. Secondly and most importantly, the Plates used to create the Jewel of Life included the Zap, Meadow, Earth and Draco Plates - which are all the types that resist Electric.
- The Grandfather Paradox that occurs when Arceus nearly dies in the past, prompting Ash and co. to fade away logically should come about as well when the Jewel of Life is returned in the past - either way, Arceus doesn't have a reason to attack humanity in the future, and Ash and co. have no reason to travel back in time in the first place.
- In the last few minutes of the movie, Arceus is still angry in the future even after the Jewel is returned in the past. If he has no reason to attack Michina Town, why was he fighting there to begin with?
- Soooo, why exactly is liquid metal as effective against Arceus as throwing a meteorite at it? Not much is stopping Arceus from using its Flame Plate to melt or evaporate it. Or using its Spooky Plate to possibly phase through it. Or, if it's mercury that's poisoning it, using its Toxic Plate to make it immune to poison. Plus, as the original timeline indicated, it had no problem with killing everything if it needed to...
- There's no indication that the Plates can be used this way. For all we know, they're completely interchangeable amplifier artifacts whose only unique abilities are type changing. They don't grant Arceus any special powers unique to each Plate, but rather the more of them it has, the stronger and more powerful it becomes. At most it could use Toxic Plate or Iron Plate to protect itself from mercury poisoning, but it would still end up encased and slowly suffocating, not to mention continuously fried with thousands of volts. And while it was able to escape and kill everyone inside in the original timeline, it was only because they underestimated its power and stopped attacking far too soon, as well as deeming the usage of Silver Water unnecessary. In the changed timeline Marcus instead has his Pokemon continuously electrocuting it until it's halfway covered in Silver Water and too weakened and depressed to fight back.