I always use the 3D, only time I've had it off is when I'm playing RE:R and aiming with the gyro (doesn't work too good when you're moving the screen and I didn't feel like moving to a swivel chair) Flipped it back on for cinematics thoughI've been there, and in not being able to drive your car higher than first gear, your car is useless.
The 3DS functions perfectly well without 3D. I rarely even use it on mine. It's more like driving a perfectly good car and just not being able to use the radio.