Yes, Nintendo did cause confusion, as evident by the plenty of people I know who were unsure what, exactly, was going on with the system, confused as to whether it was a legitimately new platform or a peripheral for the Wii. These people are not the kind who go over E3 with a fine tooth comb or intensely follow every piece of news that trickles out.
Nintendo's E3 2011 Wii U reveal was an absolute mess, and I'm struggling to fathom how an argument could be made otherwise.
Unless you stopped watching the conference right after the controller was shown, you'd have to be a complete moron to think that it was a peripheral. Nintendo did fail to make it clear because they never brought out the console (which was the ONLY mistake they made other than maybe not saying "Wii U is a new console"), but it was far from "an absolute mess." If they had just shown the controller, said nothing about a console at any point in the conference, and never said anything about any games, then I'd agree that it was a mess. As it stands, they made two small mistakes that had significant repercussions.