You can create a custom appearance, but the actual NPCs have to be one of the existing factions. So pick which enemy group has the type of attacks you want your enemies to have, and then place a spawn of that group and give them all the custom costume you created.
Having the option of having a NPC follow you would be awesome! You could assign him the same tech as a BOFF - or even replace a BOFF with a custom NPC. Which brings me again to the away team limit option.
Also, when speaking about giving NPC groups a costume: It would be great, if you could assign a costume to an entire group and have the game randomize only race, gender and head.