Shantae
Shantae director Matt Bozon has revealed that there were plenty of prototypes of games for Shantae that never made it off of the drawing board. These include things such as a spline-scroller (like Namco's Klonoa), a open-world 3D game (similar to Super Mario 64), and a 3D platformer. He even hinted that they were going to be released for the PS2, PC, and Nintendo Gamecube. Matt Bozon states:

"We had a polygonal Shantae that could be run around in three distinct gameplay 'gyms'. One was a spline-scroller (like Namco's Klonoa), one was a free-range 3D like Mario 64, and the last was an isometric 3D platformer. We've done a lot of exploration in this area" Shantae was a sprite/3D hybrid for PlayStation and PC, and was free-roaming on the PlayStation 2. She even rode a river raft on the GameCube. It's possible that we'll see a polygonal Shantae down the line, but only if it serves the style of gameplay we want to create at the time."
Contributed by CLXcool
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Before Risky's Revenge for DSi, Wayforward was developing a Shantae game for the Game Boy Advance called Shantae 2: Risky Revolution, also known as Shantae Advance. The game was about 50% completed before it was cancelled, and some of the game's graphics and ideas were reused for Risky's Revenge.
Contributed by Mass Distraction
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The first Shantae game was initially designed for the PC or consoles comparable to the PC, such as the Sony Playstation. It differed significantly from the later Game Boy Color release in 2002, as the first design had plans for using 3D gameplay/environments with characters being sprites, as well as a number of features like being able to buy new hairstyles which would each give different attacks aside from the standard hair whip, various outfits that could be bought giving different effects, and summoning (as opposed to transforming into) animals such as a Monkey, Tiger, Elephant and even a Spider to help solve puzzles. Shantae herself also looked different, most notably her hair being black, as opposed to purple.
Contributed by G-Haven