Game freak purposely makes graphhically underwhelming games and resists giant leaps in tech.
Well... Just because development is being unified in regard to platform doesn't necessarily mean that it has to be unified in regard to output. Game Freak could conceivably put out games meant to be played on the go using similar assets as current Pokemon games. 2D Zeldas could still exist as well.
I think the idea was to have one platform, not one application target. Lower-priced portable-only games could exist beside console style games that can also be played on the go.
Some devs could target HD console-style games and downscale rez for portable play (for example,) while others could simply target the underclocked portable performance and have pricing and dev cycles that reflect that.
Now whether or not Nintendo WANTS that is another story.