This has been an ongoing thing since beta, I don't think cryptic has gamers to fully understand how a joystick is suppose to work ingame. I opted out by using my old logitech profiler instead of the joystick option ingame because number one it doesn't make sense. If you are using all your buttons on things like: accept, exit, and whatever then how are you suppose to bind real UI powers to them?
I fail to see why this joystick option is here...It does not detect the joystick at all. Sure it tells you which stick you are using but what does D-pad have to do with a joystick? That's a gamepad command not joystick. It has been years now and for some reason I don't believe this will ever be understood by this company. Kind of sad though they could have implemented a lot of cool stuff in this game to make it Number 1 years to come instead they seem to have taken the easy way out and just made a total mess out of it. Simple rule for any game company: 1. Game detects joystick. 2. Game uses basic structure of joystick's brand name. 3. Let players input their own commands for joystick. In other words they really did a poor job of their joystick option. And if you got some way out long winded workaround then I hate to tell you this but that should not even be the case at this point.
I would have loved for them to experimented with voice commands while a player is in his/her ship, I use it and it's fun. Nothing like commanding your ship by voice "Shields up" and you get a feedback of whatever you type which in my case is "Emergency Power to shields: Engaged".
STO automatically mapped the basic ship movement commands. But only that.
To simplify my previous explanation.. It's really only a 3-4 step process, and for the first few steps you don't need to do the buttons individually. It's only the last step that needs to be handled individually. I say 3-4 because while 2 of the steps are technically separate you can do them simultaneously. Also those two steps are really there just to make sure the game has all of your buttons associated with something(mine didn't). If you want to save time you could just open the joystick config file and use the left column entries to map to... this reminds me.... I didn't explain how to find that....
After you save the configuration file, find the file in the live folder mine is: C:\Users\Public\Games\Cryptic Studios\Star Trek Online\Live. It's named controller.cfg.
And, you really only need to do it once. Then you can just save the configuration and keybinds and load it on all of your other characters.
I use this: http://joytokey.net/en/ program to play with a joystick on STO. Though I only really use it for space combat. It has proven to be a bit buggy in my estimation. However, it is easy to use and works well. I even managed to set up autofire on it. Which sometimes make my character jump up and down when on a ground map. But that is a small price to pay. Oh also it is not freeware it is shareware, so every once in a while it will nag you about buying a licence. So far I have been able to use it without doing that though.