I've had time to think about this, and to be honest, I can live with it. Like I said, my only problems with the Wii Mode we currently have is that we are limited to a few Megabytes of virtual system space, and it takes a short while to swap between modes, but as long as my VC and WiiWare games are safe, I'm happy.
Who's to say when Nintendo releases their next console, they won't let us transfer everything over (as convoluted as it was) from the Wii U to the new console like they did the Wii & Wii U. That was pretty generous.
I will say one thing - this Gamepad play featuire - the unique selling point of these upgraded VC games: Wasn't that supposed to be implemented at launch?