To date, my favorite Trek game remains Klingon Academy (after the patch which fixed the "ramming bug").
The user interface, when augmented with a voice control (I used, and still use, "Game Commander" for this purpose) was as close as I've ever seen to "real starship command."
The user interface is based upon verbal orders. Bridge Commander did the same thing but in a way which was unfriendly to verbal control. In Bridge Commander, you have to use the mouse, pan around, etc. But Klingon Academy used numbers.
So, number 1 would take you into the "Engineering" menu, then (from memory here) number 2 would take you to the "impulse power" controls, then number 3 would take you to 1/2 impulse.
So, I set up a voice command, so that if I spoke the phrase "Engineer, set one-half impulse" the keypress sequence (esc)(1)(2)(3) would be sent (the escape exits any prior menus).
So, in gameplay, I'd say "Engineer, set one half impulse" and the engines would go to that, and the engineer would report "1/2 impulse power, sir!"
DAMN, that made for an engrossing game.
My preferred approach was to keep my hands off the keyboard as much as possible and TRY to do everything by voice. Occasionally, I'd need to use my keypad (NEVER the mouse, much less a joystick, unless there was no other option!).
So, I'd give the helm standing orders, give the gunner standing orders, and just do things as they came up. PERFECT game structure.
And the production quality (less the "ram'em" bug) was outstanding. It runs perfectly today on my current system, but you MUST disable your "windows" keys... otherwise you should just expect to kill the game every time you accidentally tap the (essentially useless anyway) windows keys.
Very few games still hold my interest like this one. The first two "Thief" games... anything in the "Half-life" series... the EARLY "Rainbow Six" games... and Klingon Academy. Few other games come close.