I haven't had any issues at all with Bit Trip Saga.
You have to put up with the control scheme imposed on you but that's about it. And that issue is not different than the Wii versions, but the imposed controls are different, so it comes down to preference.
For example, Bit Trip Beat:
- controls on the Wii by tilting the Wiimote,
- controls on the 3DS with either the control pad or stylus on the bottom screen. Of the two, I find the stylus easier to control, but neither is "ideal". Then again, neither was the Wiimote tilting.
The games are still good and its nice to have them all portable, all in one place, always on your system and at a very good price. Its worth it just to have Runner alone. The rest is like gravy.