The Virtual Boy had a great concept at its core but they took it in a completely wrong direction, namely making it a portable system. Or rather design it to pretend it was portable, which it clearly wasn't.
It would have been best to apply its stereoscopic 3D vision to a home console, as optional ideally. This would have allowed it to have colors and generally better hardware, capable of full moving polygons (like thos used for the title of VB's Mario Tennis), not to mention sparing us the plague of fitting the damn thing with 6 AA batteries. I daresay that could easily have left an enduring mark on the industry. Especially if they gave it the N64's analog stick.
Now it seems after all these years, Nintendo is again going to try and play the 3D card (most likely due to all the hype around 3D movies that has swept theaters worldwide) and once again they are doing this with a portable system. Let's hope this time it goes better.