I'm currently using a Logitech Extreme 3D Pro to play Oolite - which involves some messing around with deadzones to stop me drifting off course in a maddening fashion.
However I insist upon using an Xbox 360 controller for things like Assassin's Creed 3 and Skyrim (never thought I'd say that being a long time PC mouse/keyboard FPS gamer) - which with its analogue sticks probably lends itself pretty well to a flight/space sim.
Having said that, the Elite I remember from the Amiga was made for digital joysticks/keyboard, so this analogue stuff is quite novel and fun for me!
I'll be testing it with both, but I will lean towards combining the Logitech and keyboard, because I love the feeling of having a load of buttons to press to modify shield settings/speed etc - it appeals to the Trekkie in me.
Of course, were a tablet-based touch-sensitive interface for managing systems settings to be developed...
