I don't understand the hate on controllers. This is the sort of thing they were invented for in the first place.
I use a PS3 Controller using the same Motioninjoy software as the guy above. I use it because when I play, "I am chill". I sit in a recliner and play on a 60" HDTV using the Controller and Wireless Mouse KB setup sitting next to me. Sometimes I am drinking or otherwise as well. This is entertainment, not a profession.
Screw that nonsense about sitting at a computer desk and putting unnecessary stress on myself trying to hit all of these KB keys and manipulate everything with the mouse.
I originally tried the native STO controller support and it didn't take long to realize there's simply too much to try and do with a gamepad.
However, since I use pinnacle for some other games I decided today to try the controller profile for STO.
I found that if I combined commands for mouse look and shooter mode to the same button it actually made ground combat a lot better especially when using the over the shoulder camera zoom. You could easily spend an hour or two trying to get the key binds exactly the way you want them, but even with combining as many commands as possible there's still things your going to sacrifice.
This is actually where a feature of Neverwinter could really be of use for STO. In Neverwinter you're locked into their equivalent of shooter mode until you press ALT which gives you control over the mouse pointer for all your menu needs. This would allow you full access of the skill tray and everything else without having to resort to still using a keyboard as well, but STO has no similar option at this time. I still find for space combat that the old keyboard and mouse is the way to go.
STO would really need to implement a voice command feature to really make full use of a controller.