You're going to want to have "target nearest attacking enemy" instead of "target target's target". Being able to target whoever is on your ass shooting at you is kinda important. You'll also want to be able to target the next live bomb or bomber, and you'll need to be able to target ships on your escort list. And not to forget, subsystem and turret targeting, if you don't have that on your joystick.
And there's probably no need for auto targeting if you have "target next closest hostile" as auto targeting just does that after your target stops being targetable(which is usually a few seconds after it's destroyed or if it jumps away).
You're missing a whole bunch of engine controls. Basically, all of them(speed matching, afterburner, turning off engines are the main ones). And once you start playing mods you'll need gliding, reverse thrust(the throttle on your joystick just won't do), and side thrusters(if your joystick has a hatstick you should be fine).
If you want to play on higher difficulties you'll need weapon->shield energy transferring(it's different from energy management because it immediately drains your weapons and boosts shields instead of just boosting the regeneration rate).
You might want to have padlock view, as it's useful to see where your target actually is.
And if you're the type to lose yourself in the glorious slaughter and zone out you might want to have the mission log accessible(default is F4), as it lets you review messages and events.
That's all I can think of now, but you might want to add a few empty buttons just in case you need them later.
