According to Japanese website Famicom Plaza, Nintendo said that the change was made to differentiate the two games. Some gamers might have trouble discerning which version is which. All three versions of Nintendo + Cats have new box art.
New, horrible looking box art. In an effort to differentiate something, Nintendo has made the game’s box art looks worse.
(0630)[(3DS)nintendogs+cats] 新しいパッケージになったのは間違いを防ぐため? – ファミコンプラザゲーム最新情報ページ [ファミコンプラザゲーム最新情報ページ]