We've known about Wii Mode and why it exist for a while now. The WAD files used for the Virtual Console games are specifically designed for the Wii, which is why you're forced to run through this mode. It's a relative nightmare splitting the Wii Shop Channel and the Wii U's eShop, especially if they end up asking people to buy the same titles once more on Virtual Console.
I'm not sure how temporary it is either. Nintendo doesn't have a great way to transfer licenses from Wii to Wii. So moving them from Wii to Wii U, so you can load Virtual Console games directly from the Wii U (enabling Game Pad play, easier access, etc), in the future is not going to be a cake walk.
At this point though, backwards compatibility is going to be tougher and tougher each generation. Not just for Nintendo, but for everyone moving forward. It's a scary part about the digital future we face on consoles, at least for me.