Yeah, assuming the Wii U actually takes off, I don't see the Pro controller having so many issues finding a wide audience that it needs to be packed in with the console. For one thing, if you want to play 4 player MP on the Wii U, you can only have 2 GamePads. Sure, on some games you can probably fill the remaining slots with Wiimotes, but most people will probably just buy Pro controllers.
Also, the GamePad is probably going to be upwards of $70-$80, whereas the Pro controller is probably at most going to be in that $30-$40 range. The price discrepancy alone will get people to buy Pro controllers. This isn't like the Wiimote/Classic Controller situation where you had to have a Wiimote to use a Classic Controller.