As always, your own preferences take precedence, but IMHO it is much more effective to use a mouse for controlling the view, at least. Very often you will be surrounded by foes or one will pass behind you, and you will need to turn around rapidly to locate your target. While a Cruiser may be slow to actually turn around, you can center the screen on your target, and you can keep it locked there while your Cruiser fires its broadsides.
I would try a mouse instead of a gamepad. But again, if you're sold on the gamepad you may want to investigate some other options. (Like a different pad, as others have suggested)
Another alternative might be to zoom out your view. While that might be more difficult to follow the action, you can use the previous target/next target buttons on your pad to select targets without having to actually center the screen on them.
Do you use mouse or keyboard to control your ship?
Ground uses W to move forward and S to move back, but in space W points the ship down and S points it up - you move forward or back by setting the ship speed: Q to slow down (or reverse), E to speed up, R for full speed, shift R for full impulse.
I find it easier to control my ship direction with the mouse and use the keyboard for changing speed and activating powers.
On which note, why can't I use a joystick of gamepad to control my ship? Is there some way of doing so?