Paper Mario: The Thousand-Year Door was initially going to simply be called Paper Mario 2 and feature a far different logo, one reminiscent of the original Paper Mario’s logo. There were also many unused badges. All of the partners from the original Paper Mario were going to appear but were cut-off as well. Bow and Parakarry were the only ones left. There was also a strange robot creature and two palette swaps of Screamy. Bobbery also had a prototype sprite, which depicts him wearing army gear. There was also going to be a probable mini-boss called Dark Atomic Boo. Dark Atomic Boo would be a Dark Boo version of Atomic Boo, and some have theorized that it may have been a more powerful Atomic Boo fought in the Dark Boo-inhabited Poshley Sanctum.
Also, in the original trailer, one can see a HP Plus badge that is located on a ledge beyond a moving platform which has a wall over it in midcourse (and assumedly could be reached with the help of Vivian). None of this made it into the final game (except the area where these things are, minus the things themselves of course). The trailer also showed that Item Shops would be labeled with Mushrooms rather than the Fire Flowers seen in the final game. Red Bones was initially named “Red Koopa Skeleton“. In the same trailer you can see that “Tornado Jump” was initially called “Hurricane Jump”. [Info from Mariowiki]