Update: Sure enough, Nintendo has told us it has "not made any announcements about the SKU." In other words, whether or not the rep at E3 meant to say it, Nintendo is not officially stating that the Wii U's controller will only be available with the console itself. That's no guarantee that it will end up being sold separately. For now, though, there's no reason to panic.
Original Story: We've seen Wii U multiplayer demonstrations where one player uses the Wii U's new controller while several other players use Wii remotes to play on the TV screen. There have yet to be any demonstrations of multiple Wii U controllers being used together, and at this point it's unclear that the system is capable of connecting to more than one tablet controller at a time. According to a Nintendo representative at E3, the system's controller will only come bundled with the system and is not going to be sold on its own.
"Both the controller and the console will be sold as one unit," the spokesperson told CVG. "You won't be able to buy the controller alone."
The rep went on to explain that multiplayer games are being designed to facilitate the aforementioned scenario, with one person on a Wii U controller and others using Wii remotes. It's possible that other controllers will be used besides the Wii remote, as the system is fully backwards compatible with Wii controllers, accessories, and games.
1UP has contacted Nintendo to find out if the rep spoke in error -- it wouldn't be the first time something like this happened with regards to a system that's still likely at least a year away from launch. While we're still waiting for the official line from Nintendo on the matter, I'm not alone in thinking that it's strange that such a decision would be made prior to things like the release date, price, or any number of other aspects being announced.