I am leaning towards no AI empires at this point. I am just thinking there will be too much that would go wrong with the AI to try and trust them. It would require me to break one of my own rules about playing multiple empires in a game, but well...
I'm thinking the Imperium race, a pirate race, and a civilian race. The civilian race will just be unarmed transport ships flying around. Basically targets for the pirates and players that wish to go bad. I am doing that so the players can prey on the civilians if they choose without nessecarily breaking their treaty with the Imperium. I intend to role play things so as long as an Imperium ship doesn't actually see you attacking a civilian you won't definetly be tagged as a pirate. You'll have to attack an Imperium vessel (suicide) or be really blantant about attacking civilians. Just remember pigs get fat but hogs get slaughtered.
Of course attacking pirates will be encouraged, and attacking other players will be tolerated, unless they happen to be carrying cargo/passengers that are important to the Imperium.
Refueling will be done at the Imperium planets. You will have a military alliance with them at first. As long as you keep that you will be able to refuel. You could also buy solar cells or quontum generators.