Nintendo thinks a bit differently, so it's hard to say why they left out cross-game chat. It wouldn't surprise me if they thought certain games, such as their own, would be hurt by people chatting.
My guess is that, since cross-game chat is only on the 360, it's only something a western gamer would consider important, and Nintendo, being quite Japanese-centric, just didn't consider it as anything more than a novelty. I think it's really just a simple cultural mistake more than anything, and perhaps that they didn't do enough research into the western market. Of course, it could also be Nintendo being somewhat arrogant after the success of the Wii, believing that Nintendo fans will buy whatever they are presented with--and some of them will.
All that being said, it could potentially be something Nintendo has viable workarounds for, or that could be added later. This might very well be a non-issue ultimately. However, I do think Nintendo should clarify or address this, because, like it or not, it is something that a good number of people would like to see on the Wii U.
