The WiiWare release will include extra features and things to do, and apparently will be released on WiiWare's launch day for 1000 Wii Points. Ubisoft's James Regan told IGN:
Ubisoft is excited to bring Protöthea exclusively to the platform and we feel it's a must-have WiiWare title," shared James Regan, vice president of third party operations, Ubisoft. "Protöthea really reminds me of some of the best arcade games, with the Wii Remote as an added dimension. It's just a flurry of fast-paced action that anyone can simply pick up and enjoy.
Check out the video and screenshots on our Protöthea page.