Yeah, I'd be concerned about controls, but it would be worth a try. Plus, the original Descent had support for VR helmets, which were stereoscopic, so that might make a port to 3DS easier. I never had a VR helmet or knew anyone who had one in order to try Descent on it, but I would imagine Descent would be insanely sweet with depth perception.
I wonder if the touch screen could be used? Maybe for weapon selection? And to show the cockpit so it doesn't take up room on the 3D screen? Of course some may want the "F3" option and see the cockpit in 3D.
Let's see, off the top of my head... anolog control for aiming, accelerometer forward/backward for slide up/down, accelerometer left/right for banking, shoulder buttons for sliding left/right, ABXY buttons somehow for forward/reverse and fire primary/secondary, D-pad for less often used functions like flares, and prox bombs, touch screen for weapon selection... It could work... I think they should keep the options for fully customizing the controls, though, but maybe come with a couple presets that playtesters liked.
I just had an awesome thought: Automap in stereoscopic 3D!