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Yes, the game saves tie to your personal NNID.

With the exception of I think one game (NSMBU Nintendoland)... if I remember correctly. I think that one still shares the three saves across all users. Likely because it was such an early game and they didn't get around to updating the Wii code on it.

But every other game I've owned keeps all of the saves separate. (see my sig for the games I own)