Yeah, I wonder if it really is that difficult to do... well, I'm sure it's possible. Maybe they think the effort isn't going to be worth it?
Coming from a programmer background, I honestly don't expect it to be *that* difficult to do. I'm not sure how the WiiU, 3DS, or Twisted gyro sensors work, but I assume that when they detect movement, they just calculate some numbers which state how much it rotated on the X, Y, and Z axis (aka: yaw, pitch, and roll, for anyone familiar with those terms). To emulate it on either 3DS or Wii U, Nintendo would basically need to translate these XYZ values into ones that the Twisted gyro would send (which I also expect would follow the yaw, pitch, and roll concept), making the WarioWare game *think* that they came from that hardware.
Seeing as they're all probably just float values (basically just numbers with a decimal place), I doubt there'd be much difference. If Twisted gyro has a smaller number of decimal places then they can just round off the WiiU/3DS values (or if it is the other way around they can just add zeroes to the end of it). Pretty simple math to calculate and program, really.
Though this is all conjecture and kinda assumes Nintendo weren't retarded when they developed either hardware.