It would be cool to see Daisy in a Paper Mario game huh? Well now you can.
THIS MEANS SHE IS CONFIRMED TO APPEAR IN A NEW PAPER MARIO GAME?! :D
...No, but you can have her in a different way:
There is a unoffical remake of Paper Mario Color Splash, Paper Mario Color Splash Recut, it features tons of different characters including Daisy.
http://forum.mariorpguniverse.com/thread/565/paper-mario-color-splash-recut this is an example, there are others in various websites like Marioboard and Gamefaqs.There are some sprites for invent your own Paper Mario story as well, here is Daisy:
And here we have some examples on Daisy in.