What about DSi and 3DS?
There's no successor to 3DS yet, so we don't yet know how they'll handle 3DS backwards compatibility. As for DSi, I don't have one so I have no idea how it works, but since it's still in the DS line then I just figured it's a lot more simple than the Wii menu, and therefore it was a lot easier to get DSiWare games to run without making a DSi Mode. The DSi is also a lot newer than the Wii, so it was probably designed a lot better to begin with, and was likely designed with 3DS in mind since they were surely working on it at the time.
Also, for the record, I'm not saying it's impossible to better integrate Wii Mode into the Wii U, I just think it'd be more difficult than it seems, and so I think they won't. Though if they plan to continue selling Wii games or release some as downloads, they probably should make it better.