I don't think the WiiU "confusing upgrade vs. True Successor" siituation is quite as bad as it is with the 3DS (particularly since it's not even out yet!) but I think the potential for people to not really understand it as a brand new system is there. The "Wii X" name has applied to games and peripherals for years: Wii Sports, Wii Fit, Wii Music, Wii Sports Resort, Wii Play, Wii Play Motion, and the Wii Balance Board and Wii Zapper are all things that you use with the Wii. That makes sense. It also doesn't include the likely dozens of games that start with "We" in a thinly veiled attempt to cash in on that branding power.
Now there's going to be WiiU, and the reveal was focused almost exclusively on a brand new controller that they showed playing existing Wii properties, including Wii Fit, various Wii Sports and other Mii-focused minigames, and a game confusingly called, of all things, New Super Mario Bros. Mii. And this is after Nintendo has released a line of dual-screened handhelds called the DS, DS Lite, DSi, DSi XL, and 3DS, all of which (sans the 3DS) are gradual upgrades of each other.
I think you have to admit that there's a massive potential for confusion as to whether the WiiU is a "new system" or not; nothing's set in stone, but when the ducks are lining in a row like so, and people have (rightly, IMO) criticized Nintendo for not clarifying the 3DS's identity as a "new system," I think it's natural to connect the dots and wonder if Nintendo will do the same for WiiU.