Great! Thanks a lot guys. I was able to make Titan and Starbase duplicates, and it's worked well. I really like the idea of using pirates or a special pirate ship to give increased amounts of experience to the militia as well. I didn't think of that!
As for the upgrades, I was unable to find out how to designate a the duplicate's upgrades via the .entity file. Where should I look if, for example, I wanted to make a Transcendia Starbase with the "Meteors" ability? Would the NPC even use it? I have, in playing since Entrenchment came out, never seen an Advent starbase use meteors. If that is not possible, I could, of course, just upgrade the hull, shields, and dps of the duplicate to increase their difficulty, but that's a "cheap" workaround I would like to avoid if possible.
Thanks again for the help.