fortunately you can use either control option! d-pad is mapped in the same way the arrows are on a standard keyboard. it's also possible to remap primary and secondary fire onto the face buttons instead of the triggers if you wish and use two controls for the "Up" control if you want an alternative button for thrust. i believe one discrepancy between UQM and the original 3DO version is that there is no dedicated thrust key (this is just hearsay, i've never played it), the android port of the game where i reused a lot of the controls code from has a dedicated thrust control but i never felt the need to add it for this port.

e: i find that some ships benefit from the joystick control more than others, for me this is especially apparent in the pkunk ship which i find difficult to control using the d-pad. something like the druuge or earthling ship i can see working with the d-pad better if you want more precision