The working title for this game was Super Mario 64×4. Also, several beta screenshots were released for the game. Originally, all four characters could fight Bowser at the same time, and fly. This feature was removed, as the four characters can only fight Bowser by their own (with Yoshi utilizing hats to be able to swing Bowser).
Also at E3 2004, there was a demo called Mario’s Face, where the user could use the stylus to mess around with Mario or Wario’s face, and have them be 3D or outlined like a cartoon. This could have possibly been the beta Mario Mini for Super Mario 64 DS. The caps the player uses were originally enclosed in boxes labeled M, L, and W. The boxes can still be found in the test level.
Also, early screenshots depicted Wario with his original long shirt sleves before adopting the shorter ones for the final product. The game was also originally was supposed to have a co-op mode but was canned probably due to memory constraints. [Info from Mariowiki]
An unused Red Koopa model was found in the game’s code with some cheats.
Thanks to Hiccup for the contribution!