My only problem with the FSS is you need an axis for it, preferably one that isn't self centering like a joystick. You can tell where each type of signal is going to be on the tuning scale. Each type has its own place on the scale, the stronger the signal i.e. the stronger the gravity well, the further right the signal will be on the scale. If it weren't for an axis being required, I'd be all for it as it will save you the time of not having to fly to each planet.
A gamepad actually works remarkalby well for FSS, and feels pretty good doing it. I use a HOTAS for the game itself though and can't be bothered to switch back and forth. What I settled on is using my throttle for step tuning and the U-axis that is on the throttle handle for regular tuning. I use the mouse for moving about and zooming in and out.
I have the hat and joystick of my flightstick configured as well, like what @Stigbob indicated, but I find it awkward and slow compared to the mouse. My mouse is just to the right of the flightstick so it's simple enough to just use that instead.