Rayman no longer loses health from drops into bottomless pits.
Lighting is brighter in most levels (most noticeable in the Sanctuary of Rock and Lava and the Iron Mountains), and the lighting/shading on Rayman's model is no longer affected by light sources.
The original plum texture can be seen on part of the new model.
The plum is now a 3D model as in Rayman 3, rather than the 2D sprite seen in all other versions.
The Powder Keg now uses a higher-poly, rounder model.
The Stone of Thought, Purple Lum, and ledge leading to Globox Village in the Dreamcast version were removed in the 3DS game.
It however does not have the minigames from the Dreamcast version.
Rayman 3D is built off the Dreamcast version of Rayman 2, and shares the same Isle of Doors hub level as well as most exclusive cheats and graphical enhancements.