The Analogue stick is probably the only thing that REALLY sticks out and was a major design oversight.
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.