The Analogue stick is probably the only thing that REALLY sticks out and was a major design oversight. But that's also not new. The GB needed the GBC to make up for going a bit TOO cheap. The GBA needed the GBA SP to light the screen.
I think functionally the 3DS actually works rather well. Only a few games needed that second stick badly since...well games designed for it were designed usually for single stick play. The screen quality is the more jarring thing for my personal taste. They traded too much there for the 3D. And I actually like the 3D.
I haven't really followed Nintendo's handhelds as with the exception of 3DS I never owned any. It's just that in isolation the 3DS just seems to me a poorly designed piece of hardware. Switch for example is vastly superior in concept and execution.