Sami would be great...she is easily the most recognizable female from the series.
Paula would work. I forgot to put her on there, and then saw it mentioned by others, so I figured I would leave it be.
Midna: I may be the only one, but I really do not want a Wolf Link in the game at all. That leaves her in her imp form alone or as the full restored "Princess" version of the Twilight Princess. Either of those could work well...but my favorite idea would be to replace Sheik with a turning into the Twilight Princess and Zelda, but they are the two Princesses in the two realms, but I don't think that idea would work well.
I don't know Lip very well, but I do agree that the Koopa kids make better Assist trophies, specially if one of them can turn players into an animal temporarily.
As for the rest of my list, you could of just added on to it...and not taken away. There is nothing wrong with Daisy.