The Pokemon lore is forever changing with each new game. As the series currently spans eight generations, it would be understandable if old pieces of lore were forgotten or contradicted with the newest generation. Pokemon Legends: Arceus builds on the beloved Sinnoh region, but it also piles on new information that contradicts what the Pokemon world has already created.
Some lore differences between Pokemon Legends: Arceus and entries that take place in the "present" (such as Pokemon Diamond/Pearl) can be potentially be excused as the Pokemon world evolving. However, other differences are a bit more glaring, and have already drawn more than a few question marks for certain fans.
Warning: Late/End-game spoilers for Pokemon Legends: Arceus
10 Pokedex Entry Research Tasks
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For the first time, Pokemon Legends: Arceus requires trainers to "unlock" a Pokemon's entry. This is done through "Research Tasks," which range from catching a set amount of Pokemon or seeing it use a particular move. Never before in the history of Pokemon has the act of seeing a Pokemon use a move been required for a Pokedex entry.
However, since this is meant to be the first Pokedex ever recorded, observing a Pokemon's moves could be seen as a way of researching the Pokemon's Ttyping, learnset, and more. Since Hisui doesn't have modern technology, it's possible that Professor Laventon needs as much data as possible before he can write an entry. Or, in a meta-sense, perhaps this is Pokemon's way of temporarily putting aside the Gym Leader challenges that have been a staple in the Pokemon mainline games since the beginning.
9 Pokemon Have Different Learnsets
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Some of the moves that Pokemon learn upon leveling up are very different from what they may learn in the main Pokemon games. For example, in most games Eevee learns Bite, a Dark-type move, but in Pokemon Legends: Arceus, it's incapable of learning the move. However, the move still exists in the world of the game, since other Pokemon can still learn it by leveling up. Instead, Pokemon Legends: Arceus has Eevee learning Calm Mind, a move that it was incapable of learning before.
It's highly possible that Pokemon in Hisui learn different moves from Sinnoh Pokemon, because Hisui itself has a completely different environment. Perhaps Pokemon like Eevee grew to adapt their moveset over time.
8 All Evolution Items Functioning Like Evolution Stones
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Except for the Linking Cord, which is an obvious reference to the original methods of trading Pokemon, all Evolution Items in Pokemon Legends: Arceus work like Evolution Stones. This has not been the case in previous games, where evolution items could be used in a number of ways.
Some Pokemon must hold an item to evolve, such as Happiny, who evolves into Chansey when it levels up during the day while holding an Oval Stone. In Pokemon Legends: Arceus, trainers need to simply "use" the Oval Stone on Happiny to evolve it. From strictly a lore perspective, if Oval Stones were once Evolution Stones in the past, what caused them to change over time?
7 The Lake Guardians Can "Talk"
Talking Pokemon are not a first in the series. In fact, some Psychic-types are known for being able to communicate telepathically with humans, especially in the anime. The Pokemon in the Mystery Dungeon series can all talk because the player has turned into a Pokemon, making it possible to communicate with them. Necrozma in Ultra Sun/Ultra Moon speaks one line, but it doesn't really talk to the player.
The Lake Guardians could speak in Explorers of Time/Darkness/Sky, but Arceus marks the first time they speak to a human in the games. Furthermore, the Lake Guardians have trials for the player to overcome. It was never stated before that Uxie, Mesprit, or Azelf could speak to humans, nor set up trials for humans. If the Lake Guardians appear in a future game, who knows if they'll be able to communicate from now on.
6 Alpha Pokemon
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As the name implies, Alpha Pokemon are a subset of Pokemon that are stronger than others of its species. They're characterized by their large size and glowing red eyes. Barring Dynamaxing, the idea of different-sized Pokemon isn't unheard of, especially in the anime, but it's new for the Pokemon games. Trainers can catch "small" and "large" specimens, but they're not the same as Alpha Pokemon.
The strange part is that Alpha Pokemon have never been alluded to in previous Pokemon titles. It's hard to imagine Pokemon as large and powerful as Alpha Pokemon going extinct over time — and even if they did, there would likely be records of giant Pokemon roaming the land.
5 The Diamond & Pearl Clan
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In Pokemon Diamond/Pearl and Brilliant Diamond/Shining Pearl, speaking to NPCs reveal that not everyone really knows who created Sinnoh. In Diamond/Brilliant Diamond, people will say it was Dialga, while in Pearl/Shining Pearl, they'll argue Palkia.
The Diamond and Pearl Clans are brand new to the Pokemon world, and are an obvious reference to the in-game debate of Sinnoh's creator in modern-day. However, there are no records about the Diamond Clan or the Pearl Clan in Pokemon Brilliant Diamond/Shining Pearl. This is odd, given BDSP's reference on how to get Manaphy in Pokemon Legends: Arceus.
It's possible that the Diamond Clan and the Pearl Clan have been lost to history. While they provide an interesting, close-up look into Sinnoh's lore, their addition seems to be strictly for Pokemon Legends: Arceus' story more than anything else.
4 Hisui Starter Pokemon
Hisui is ancient Sinnoh, so it's strange that the Starter Pokemon were not Turtwig, Chimchar, or Piplup. Instead, each of the Starter Pokemon come from different regions: Alola, Johto, and Unova. Is this meant to imply that Pokemon of different regions used to live in Hisui together? Another theory was that these starters were a reference to the samurai.
From an in-game standpoint, however, Hisui's starters compared to the modern-Sinnoh's starters are a first for the Pokemon series. Most starter Pokemon in previous Pokemon games don't have such a deep meaning tied to the history of a particular region.
3 Chimchar's Pokedex Entry
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Players can get their own Chimchar by doing the Request: The Mysterious Will-o-the-Wisp. Completing Chimchar's Pokedex says that it was once known as "Lantern-tail" because of its fiery rear.
The theory behind this would fit better for a Ghost-type Pokemon, which is even alluded to in the Request, but for some reason, it was made to apply to Chimchar. This gives trainers more history to Chimchar, but it's certainly a unique addition to its species.
2 The Azure Flute & Celestica Flute
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The Azure Flute is notorious for being an unobtainable Key Item required for meeting Arceus in Pokemon Platinum. Given that Arceus is the titular legendary of Pokemon Legends: Arceus, it's only natural that the Azure Flute would make an appearance in the game. The Azure Flute itself is a mystery, but Pokemon Legends: Arceus takes this a step further by having the Azure Flute transform from the Celestica Flute.
The Celestica Flute is a special item that can call Pokemon like Wyrdeer for assistance. However, in the postgame, the player character's Celestica Flute turns into the Azure Flute. Volo alludes that this is Arceus' way of saying it wants to meet them, but it's an odd way of getting Arceus' Key Item. It's also shown that characters like Irida have their own Celestica Flute. Does this mean any Celestica Flute can "evolve" into the Azure Flute if Arceus deems them worthy?
1 Pokemon Can Shrink Themselves
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Perhaps the biggest inconsistency with Pokemon's lore is the fact that Pokemon can "shrink themselves" to fit into Poke Balls. Not only has this been pointed out before, but it does create a huge contradiction in Pokemon's lore. Poke Balls have been known to transform Pokemon into "energy," and that's how they're able to live inside Poke Balls.
Professor Laventon saying they can shrink doesn't make much sense when the history/creation of Poke Balls has been established since the beginning. Maybe this was a way to accommodate the original creation of Poke Balls and to excuse the lack of modern technology, but it still doesn't clear up how exactly Pokemon shrink.
Pokemon Legends: Arceus is available now on Nintendo Switch.