I've paid a fair amount of attention to strange Japanese games, but this situation's weird in a very different sense. It's confusing, especially if you're unfamiliar with how Japanese text works, so stay with me here.
Written Japanese uses three character sets, right? One set is "Kanji", which is Chinese characters (with the symbolic meanings and whatnot), and another set is phonetic (just sounds, no symbolism) called "Katakana", which is used to indicate "foreign" loanwords, such as sci-fi terms and anything that's not a "real" word. As you might imagine, games in the Final Fantasy series would make heavy use of Katakana, what with all their intrinsic nonsense.
That's where the issue lies. Apparently the Japanese edition of Final Fantasy XIV has replaced a portion of the "usual" Katakana-written terminology with Kanji symbols. The most telling example is the replacement of "Chocobo" (チョコボ) with the two Kanji characters for "Horse" and "Bird" (馬鳥).
This of course has confused and enraged many Japanese players accustomed to the standard nonsense naming scheme which, while unwieldy (and hilarious to hear pronounced with a Japanese accent), makes more sense than all this new nonsense.
The weirdness continues, as some terms exist in-game as written in Chinese, rather as written in Japanese, even prompting accusations that the game is secret kind of insidious port of an obscure mainland MMO.
Square Enix offered several (sometimes conflicting) explanations for the changes, including the need to "build atmosphere", and to consolidate terminology with the upcoming Chinese-language release. They eventually backpedaled on the decision after Japanese players were confused and enraged. Mind you, English-language players will have nothing to worry about. But still, this is goddamn weird.
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