Tl;DR duffmann really likes the 3D effect, thinks that's all the 3DS has going for it and is heartbroken that more games aren't using it.
Nobody cares about the 3D effect. Almost nobody uses it. Them fading it out (which btw is more a developer choice, not nintendo) is logical because nobody gives a shit about it.
Well that's just ignorance as polls on this site have shown time and time again that plenty of people still use the feature. Again, please put personal preferences aside and understand that the market is large attracting lots of different people for different reasons, one of the reasons indeed being 3D, just not for everyone such as yourself. Stupid to kill off any of those attractions prematurely is all that I'm getting at, could be the difference of selling tens or even hundreds of thousands of units.