Just a thought, while being able to issue instructions to non player characters is an excellent idea, I wouldn't like to see the game being filled with actual dialogue. I mean, I'm sure we'd all want to spend most of our time on the action rather than reading reams and reams of dialogue!
Well, more to the point, let's make the dialogue abstract.
Let's say you can issue comands by broadcasting the command or directing it to one particular individual. The broadcast command is easy enough, it gets everyone in the area who hears the command to do whatever it is you want them to do (the default command, shouldn't require a click to activate). Issueing a command to a particular indivual will of course be for those occasions where you want a specific unit, say a guard to defend an area or a specific alien to surrender (assuming it is willing and it can understand you).
The commands would be simple. Something like "Move to" (to send people to a safe area or to simply flee), "Attack", "Shout" (for distracting), "Help!", "Intimidate" (lowering morale of the more timid aliens), "Surrender!", "I surrender" and etc, etc, just to name few examples.
Targeted orders would need several clicks. First to select the person to order and then the target of the order. Some commands would bring up a yes/no dialogue such as if the aliens demand that you surrender.
Of course, the success of quite a number of the commands should also have a check to see whether or not it's successful. You can't just automatically expect an alien to surrender when asked, or else the game would be too easy!
Various factors, like the unit's knowledge of languages (maybe a simple percentage) and translation tools, the target's mental state and perhaps hostility.