The Legend of Dark Witch Wiki/Trivia/JPver

All Japanese Dark Witch Games have Zizou's voice actor saying the name of the Japanese name for respective Dark Witch game when showing on 3DS menu (International 1 and 2 have beeps while 3 is Zizou saying international DW3), and the JP version of Dark Witch 1, 2, and 3 have the characters saying FlyHigh works upon boot-up and the same rule of the game's name applies to this (INT Dark Witch 3 has characters saying Circle Entertainment, and The Legend of Dark Witch, JP is original Dark Witch name)

If talking about the gameplay, nothing much has changed, and outside of the extra voices, you're not missing out on anything.