If Miis aren't part of the actual Roster. Why can't you have a different Seperate mode that you play with Miis? (Sort of like Mario Party 8) Where there is 2 options:
1. ONLY Miis are playable (Seperate Mode, Limited Items (No FS), No online)
Where you can't have Miis against Mario, Snake, or Pikachu. Only Mii VS. Mii, Mii VS. Mii VS. Mii, Mii VS. Mii. VS. Mii VS. Mii, Miis VS. Miis, Miis VS. Mii. You can only battle with them in this mode. So no Jack Bauar VS. Snake, No Mel Gibson VS. Ike, No Eddie Murphy VS. Pokemon Trainer. But one drawback is that ther is no Online available for this mode.
2. Both Roster & Miis avaliable (Mii in Roster, But still seperate. Limited Items (No FS), No online)
This can happen, but to provide less space on the disk. They should not be able to have 3-4 players. Only 2 players at a time, and limited items. And once again, No Online for this mode.