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I've found that it's a rather contentious issue in the Pokémon fandom whether names like "Pikachu" should be capitalized when referring to the general species (and similarly for certain other words). Such as:

If your team consists of six Pikachu, you're going to have a hard time against Ground-types.

Many people who I've seen talk about the subject believe that those bolded letters should not be capital, because there are no rules to make it such.

However, I've also noticed this "special capitalization" of words in other, actually literary series as well — for example, the Dementors, Boggarts, or Hippogriffs from Harry Potter, or the Yeerks and Andalites of Animorphs fame.

Any arguments I've seen on the subject have invariably degraded into bickering about different sides of the debate. Are there any more authoritative opinions on such a phenomenon, and if so, where can I find them?

(What's special about the Pokémon case is that the species as a whole is usually only referred to by a "characteristic instance" of it — while you wouldn't say "I like dog better than cat because it's more loyal", you could definitely say "I like Squirtle more than Charmander, because it's cuter".)

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If the Ngrams are to be believed, it looks like Pokémon creature names are indeed capitalized as a general rule.

As you mentioned, I wouldn't say, “I like Dogs better than Cats because they're more loyal.” However, I would say, “I like the Italians over the Germans in this weekend's semifinal match.” Maybe the names of such fantasy creatures are considered on par with a nationality or genus, rather than a species?

NOAD says:

genus (noun) a grouping of organisms having common characteristics distinct from those of other such groupings. The genus is a principal taxonomic category that ranks above species and below family, and is denoted by a capitalized Latin name, e.g., Leo. [emphasis added]

NOTE: I'm not claiming that Pikachu or Wobbuffet is Latin, or even pseudo-Latin, I'm just saying that that the “to capitalize or not to capitalize” question might depend at which level you would put these names in a fantasy taxonomy. Either that, or, perhaps more likely, they are simply considered proper names by those who write about them.

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