The Pro Controller is expensive because Nintendo is pushing profit margins .... [/size]I expect Nintendo to still hear how "crappy and cheap" their system is considering it can't do something right out of the box that 360 did ages ago. I'm not saying I agree with that sentiment, but that opinion holds some water.[/size]
Cost IS a factor. Deciding early on they don't want a headphone jack on the pro controller means, aside from parts, a lot of considerations around layout, wireless transmission, battery life and assembly never have to be made. As you said yourself, Nintendo wants a profit on this thing, so they can sell the base system cheaper.
And please don't pretend the bits inside the Wiimote just come for free now.
It's true that they're probably gonna hear about how cheap their system is anyway. If the 360 is the comparison though, the Wii did a lot of things out the box that the 360 didn't, like WIFI and motion control, and an actual web browser. Likewise, the Wii U is not pretending to be the 360, and people can't both complain about how much the pro controller, a seperately sold peripheral, looks like the 360 controller, and then also complain about what it does differently.
In general I think people quite often confuse the two seperate issues of sound financial decisions and costomer appeal. Just because something doesn't ring quite true with the consumer doesn't mean there wasn't a good reason to do it.