If Nintendo can't/won't lower the price, then the idea of including more games in the package is a good one. Digital games add nice value without having any meaningful impact on manufacturing. If they include SmUsh, Mario Kart VIII, and Mario Maker, that'd be a nice triple threat. Might as well toss in Nintendo Land too, it's nice to have around, but something that most people may not want to pay for.
Radio chips are expensive. Thinking back, a Gamecube controller costed $29.99 while a Wavebird was $39.99. Then you have Wii Remotes at $39.99 and Xbox 360/PlayStation 3 controllers at $49.99.
Again, controllers have huge markups. Not just this gen, but for a long time.
EDIT: Also, I'm fairly certain you're off about the GCN controller pricing, if you're talking USD. When the GameCube launched, its controllers were $34.99. The WaveBird also launched at $34.99, and then the corded ones dropped to $24.99 at that time, or maybe a little sooner.
That's a good point about the Wii U using proprietary parts, I hadn't thought about that. If the architecture is different from other systems/computers/devices, and its components are uncommon parts that newer devices doesn't use, it could actually be more expensive to manufacture older/weaker hardware. There's a tinge of irony to that, perhaps.
There are a lot of unknowns here though so I s'pose we can mostly speculate based on a few facts.