It's pretty likely that Fez won't be gracing WiiWare, judging from some not-so-nice things one of the developers had to say regarding Nintendo's platform. Phil Fish, the game's co-creator, told Destructoid back at PAX East that "WiiWare just wouldn't be worth our time and effort," and described it as "a dismal system" that he avoids as both a consumer and a developer. "No demos? F*ck off," he concluded. Of course, there are demos on WiiWare now, but for years that wasn't the case.
When questioned on the possibility of 3DS, Fish commented that anything he'd produce would have to be a different game entirely -- kinda like Super Hypercube, his stereoscopic 3D game. It's hardly a confirmation, but we're fairly certain the man doesn't go around winking and nudging people, willy-nilly. That'd be weird!