Let's see...
Princess Shokora from WL4. That game is so fleshed out and well done and it just improves upon the Wario Land series by doing what Wario lacked, telling a legit story as well as adding another female lead perhaps to be the better version of the save the princess cliché.
Kumatora. She's got attitude, she's got disguises, and she's just a really well done character as well. Not to mention she's an orphan/princess... hmm I see a pattern.
Captain Syrup. She's a very fleshed out character changing the way people looked at female characters in gaming and has a personality that is strictly her own and she has only made an appearance in Shake It later on so she is fleshed out and detailed enough to deserve a higher spot on the list.
Daisy. She has an interesting personality full of attitude, adds to the enjoyment of the spinoff Mario titles, and came from Sarasa land on an original GB title. She has yet to make more appearances in mainseries titles.