Seriously, you could remove Pichu and replace it with another small Pokémon, and everything would still turn out the same. To make matters worse, the poster of the film displays it like a main cast member, even though it has very little screen time than that of other (more notable) Pokémon.
Descended Creator: According to ADR director Tom Wayland, Arceus was originally going to be voiced by actor Vincent D'Onofrio of Full Metal Jacket and Men in Black fame. However, before his recording session, there were difficulties with D'Onofrio's agent and he was unable to record for the movie. After re-auditioning, Tom Wayland himself was chosen to voice Arceus instead.
Fridge Horror: 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.
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?
When Sheena tells the heroes about a legend involving a young trainer with an electric Pokémon, Dawn automatically assumes it's referring to Ash. He isn't so quick to agree however, probably because of what happened the last time he Jumped at the Call.
Some people said that Marcus was the human version of Shadow the Hedgehog when the movie was still in Japan, thanks to their similar appearances. The English dub then had Jason Griffith (the English voice of Shadow from 2005 to 2010) voice Marcus.
Iron Woobie: The Creation Trio, particularly (and literally) Dialga. The three of them stand up against what is essentially their parent (and a literal God) to stop him from destroying humanity, and get repeatedly knocked down, with Dialga being the last man standing.note However, it's not directly said in the movie that Arceus created the three, and the trio don't seem to be bothered about attacking their creator, so make of it what you will.
Just Here for Godzilla: There's a part of the audience that skips most of the story just to see the Creation Trio battle against Arceus.
At one point in the future, Team Rocket stumble across the real Jewel of Life as Arceus battles above them. You'd think that they'd try and use it to bait Arceus and get him under their control (or at least get him to cease his "judgement"). Instead they fumble around, do nothing with it and by the end the Jewel fades away thanks to the Timey-Wimey Ball. They might as well have never found the sodding bauble to begin with.
At least one critic persuasively argues that the Damos plot would be significantly more compelling if he had originally given in to temptation and refused to return the Jewel of Life, a good man betraying his morals for the sake of what he believes is a Necessary Evil. Such a plot would also have made Marcus a bit more compelling and three-dimensional, using him first as a Devil's Advocate, and later, to try swiping the jewel himself in the endgame.
Ash, Dawn, and Brock doing nothing but standing there as Kevin explicitly orders them to escape as Giratina is in the distance fighting Dialga. Then Ash impulsively runs into the lake to get to Giratina. Granted, Giratina doesn't hurt him, but it was still a pretty dumb move when up against the enraged, 14ft tall Eldritch Abomination.
Sheena tells the Obviously EvilMarcus about exactly what is going to happen when Arceus doesn't get the Jewel of Life back. With almost no suspicion regarding his motivations, especially when he looks like Jafar's second-rate cousin and the kind of guy who'd be most likely to backstab a god. This results in nearly getting herself and her friends erased from time. Great jorb, buddy.
WTH, Casting Agency?: Large Ham extraordinaire Dan Green voices Damos, but some would prefer him to be Arceus' English voice as opposed to the nasally, whiny drag-queen voice provided by Tom Wayland.