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I am adapting the AEG system of brute squads henchmen and villains for combat purposes.

Lets think of it this way...

Brutes : Stormtroopers, Redshirts and other disposable assets.

These are the bread and butter of most security forces on board the ship. They're not supposed to live happily ever after, they're cannon fodder. Feel free to write out your combats and r/p these brutes freely. Make it interesting, make it a good read, don't make it boring and don't make it unrealistic. Remember Han Solo chased 4 stormtroopers through the death star, but ran away when he stumbled into their barracks.

Henchmen : Odd Job, Jengo Fett and the big shirtless aircraft mechanic in Raiders of the Lost Ark.

These are Henchmen, they're bigger, stronger, tougher to kill, and require more effort to dispatch. In short you can't just walk into the bar and shoot them, you need to put more effort into dealing with the henchmen. Also, Henchmen tend to be valuable sources of information, capture is better than killing in most cases. Most of the time, they get away anyway. It's up to the characters dealing with them to decide if they're going to pursue them out of the area. Bonus points awarded if you make the henchmen die from something in the game environment. (Thrown into an electrical panel, forced into spinning turbine blades.)

Villains : Goldfinger, Boba Fett & Megatron.

These are very important adversarial characters, ONLY THE PEOPLE WHO INTRODUCE THE VILLAIN INTO THE GAME CAN KILL THE VILLAIN. If player introduces his character's nemesis, and another character runs into said nemesis, the other character can R/P with the nemesis, join forces with them, fight them, have drinks, convert them to Mormonism, whatever they want. But they cannot remove them from game, it effects the plot line of the other character so don't go ruining the game for everyone else in your self righteous bloodlust.

Finally, try to remember that this is a game, and all the game world is a stage and we are merely the actors.

Technically, that's just a brute, if you see the second movie, a pair of those guys show up and are quickly dispatched, before a horde gives chase.