I think the controllers are and have been one of Nintendos greatest assets. They always have the most comfortable controllers from a design standpoint, and each new system has brought some type of innovation. I think the next system should improve on the Wavebird. The only disadvantages to the Wavebird over standard controllers is changing batteries, and lack of a rumble feature. I think these can both be solved simultaneously. Just set them up to be rechargable, like the SP, and batteries running dead should no longer be a problem. I'm sure it would be easy to set the controllers up to dock with the system when not in use, or just have four short cords to plug them into when not using them.
Once running out of batteries is no longer an issue, rumble can be added back in. Even if battery life is cut down to 20 hours (from the current 100), that is more than enough time. Chances are, you won't be playing to often for 20 straight hours without recharging.
I also think the next generation Wavebird reciever can serve as the new GBA link. The new DS will have wireless communication. If it were to be along some of the same channels as the Wavebird, no extra link cable would be needed. They would only need to add a transmitter function to the cube itself (but as that would be necessary for rumble feature, I'd be hoping for it anyway).
Also, with all controllers being wireless, there would be no need for controller ports. There could still be ports for memory cards and such, but you would free up the space on the exterior of the case that had formerly been used for the controllers. This could allow much more room for a sleek and creative design of the system, or allow for some more features without too much clutter. If they wanted to go for style, they could just have a ring where the controller port would be. When the controller is sending signals, that circle would light up, much like the circles around the Q's controller ports.