Flipnote Studio for the DSi has a vulnerability that was (relatively) recently discovered which allows custom code execution (aka ugopwn & Flipnote Lenny).
The reason for the Japanese version (more specifically, the v0 JAP) is that it's the only Flipnote version that doesn't require a save file, and that's important because, being that you're injecting into the DS DLP, which doesn't have a save file, you
can't inject one either. If you were to inject the USA/EUR Flipnote (or even newer JAP versions), you would get kicked to the home menu before you could do anything.
For the same reason, Sudoku or other games aren't used, because those need a savefile too (and the actual exploit is "saved" to the savefile, so there's no way you could use those)
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Nothing, it doesn't make any sense ¯\_(ツ)_/¯
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You can also check
zoogie's notes which provide the same explaination