Though I've been playing video games since they first came out and have been using a computer since the Mac, I never had any hand or wrist problems till this game. I now wear a wrist brace on my right hand from the never ending phaser firing. I think phasers should be automatic and we can do torpedoes manually.
There is an autofire, go into options and go to the bottom of the Controls tab, change it to one of the options. After that right click any weapons you wish to autofire (they should now have a green boarder).
Or at least a more responsive UI so that I don't end up smashing buttons. Sometimes it seems as if the cooldown is swallowing the firing command even though the interface has shown the attack as ready. You often end up wasting potentially valuable seconds.
Ok make the changes listed above in the Options window, then right click the weapon on the weapon tray to set it to autofire. It will be outlined in green when it is set properly. For ground, right click the weapon attack on the hotbar, and it will be outlined in green when set properly.
Autofire on the ground is complicated. Once you have it set, you need to fire it the first time to get it to autofire for hte rest of the mission. The problem I have with it is, on those occassions when you want to be sneaky (like when you want to scan decalithium, but don't want to spend an hour fighting everything in sight), you have to remember to click it off, or you will go around alerting everything on the map to your presence.