I'd argue the 3D effect proved to be a bad design feature as well, based on the poor market reception. curl-6 is correct to note that 3D stopped being a selling point really quick, and even a lot of Nintendo's own games abandoned it by the end, to the point where later iterations of the hardware couldn't do 3D if they wanted. There was a very literal and a figurative price to that feature though. Ultimately, I think the system would have been much better off without it.
That's indisputable, although last year we've had a thread on this site that claimed that the sales of the 3DS vindicated the Virtual Boy because stereoscopic 3D succeeded. The really frightening thing about that thread was that half or more people who posted agreed with the thread.