In the E3 2009 trailer, after Mario saves Peach from flames at the start of the game, Bowser said "How dare you!", but in the final release he says "Crud!"
Starlow was apparently intended to be called "Chippy" from the start, instead of that just being Bowser's name for her.[1]
Early dialogue
In this screenshot, the map on the bottom screen is unfinished. The mushroom hasn't been added to the Toad Plaza area.
The floor tiles have a slightly different design from the ones in the final game. The Mario and Luigi heads on the map are covered by the area border, and the map is rendered farther to the left than in the final game.
Original game logo shown at E3 2009.
Early screenshot of three treevils at Plack Beach, where Sea Pipe statue is fought.
There are various unused sound files. These include Yoshi's voice clips from Yoshi's Story, and some of the music from Mario & Luigi: Partners in Time. The PiT music won't play correctly, because it was replaced with BIS equivalent and the ones without equivalent have been replaced with "Tutorial" and "Tension" sequences. However, Yoshi voices will play correctly since they're wave files and weren't replaced or removed from the ROM.
There is an unused item that looks similar to a Life Shroom but is named Dummy[2]. If used, Mario (or Luigi) will throw it in the air (while inside Bowser) and it will explode, healing 60 HP back to Bowser. It was most likely scrapped because of the fact only the Sea Pipe Statue can damage Bowser from inside.
Some of the enemies that the Mario Bros. can't fight still have an attack pattern for them.[3]