The joystick gives a huge benefit for maneuvering and even in SC is superior for that over a keyboard/mouse. But a mouse is a superior method for aiming. It is faster and more precise than a joystick. You can get extremely good at joystick aiming but it will never be equivalent to a mouse for precision. So if a game has fixed weapons then a joystick is a superior method as it's easier to maneuver the ship it a firing position. If the game has gimbaled weapons then a mouse is better because you can sacrifice maneuverability for aiming precision.
I had an old microsoft Sidewinder - not the fabled FF version,
just a basic stick, and after a while I found the springs too
strong (I was actually in the process of heading towards something
similar but different to carpal tunnel, but to do with my wrist
and shoulder rather than the finger ligaments, and due more to
too much mousing at work than the stick), so I disassembled it
and clipped about 1/3 the length off the springs, which made it
much more gentle to handle.
As a result, I took to operating the stick with my hand resting
on the base, with just my thumb and finger holding the stick like
it was a pencil, and using my other hand on the space bar as the
fire button. I found it greatly improved my control, as I had very
good judgement of my movement from the heel of my palm resting on
the base to the fingers, as I would have when sketching a drawing.
This is similar to the joysticks for RC device control, which also
give better control than a standard joystick where the position of
your whole arm must be managed. I don't know, it may be a very
individual thing, but I find I have much better ability to control
fine finger movements than whole arm movements, despite the scale
of "full throw" distance being tiny by comparison.
Also note that I only acquired the joystick after about a year of
flightsimming using the mouse - it took that long to decide I was
sufficiently interested to invest. This also influenced my manner
of handling the stick.