The 3DS game will have completely different levels to the Wii U game.
http://www.nintendoworldreport.com/news/34469
Dimps, the long-serving handheld Sonic The Hedgehog studio, is developing the Nintendo 3DS version of Sonic Lost World.
According to the game's producer Takashi Iizuka, the 3DS edition is not a port of the Wii U version, which is being made by Sonic Team, and will instead feature "totally new level design to match the screen size and hardware so players can enjoy both versions with a fresh feeling."
In the past, Dimps has been responsible for the Sonic Advance and Sonic Rush series, as well as the DS version of Sonic Colors and the 3DS version of Sonic Generations, all of which are 2D games. Their prior experience with 3D Sonic level design is the Daytime stages in the Wii version of Sonic Unleashed.