Both games now feature "action drawing" that allows the player to draw directly in the game world rather than in an editor. Planet Moon describes expanded drawing options in this mode, like certain types of ink imbued with gravity or bounce -- like an anvil that you could draw, which would then fall straight down. 5TH Cell's drawing enhancements (at least the ones mentioned in the interview) include the ability to customize character designs even more, with up to four arms and four legs, and resizable limbs.
The games have different stories, as well -- the DS game (whose story is told in a "redone overworld" with, like the rest of the game, animation by Pirate Baby's Cabana Battle Street Fight animator Paul Robertson and art contributions from Braid's David Hellman) follows the events of the Wii game (whose story is told in a new side-scrolling hub world).
Nintendo Wii console