Make the handheld and the console one. Buy one game, and it can be played on both.
I think the dual screen clam shell design should stay. The second screen has really helped clean up the HUD in most games.
Other than that, Nintendo should ditch the stereoscopic 3D and create an HD handheld with an OLED screen and better online functionality.
I really like the clam shell design, but if I wouldn't work with the top feature, I'd be fine with ditching it.
Making the handheld and the console completely interchangeable and usable together would be my top wish. Not saying Nintendo should make a handheld and a console that you
have to have together, but, in a way similar to what the WiiU is already doing with the tablet controller it uses, if you have both "systems", you could play using the handheld as the controller, and when someone wants to steal the TV from you, or you want to go to a separate room or out of the house, you could take the game with you using the handheld. Perhaps Nintendo could offer packages that sell the two together, but also sell them separately for people who only want one or the other.
I also want them to ditch the 3D. I've honestly used it for all of maybe 5 minutes in my over 1000 hours clocked. It sometimes makes for some pretty cool cut scenes, but for the most part, it just gives me a headache. I'd much rather have HD over 3D.