AGoetz
Yeah, the hidden flag is pretty useless against the AI, though if the AI is using the Technomage illusionary ships (I'm working on a special Technomage ship design AI - though if PF wants to do the research file

), it could confuse a human player who isn't paying attention.
IF
Maybe a personal transport/flyer type thing then that will be pretty small, like between a fighter and scout. Give it some built in stuff and then you would be left to outfit it. Wouldn't be able to effectively carry more than a defensive weapon or so - if it hoped to have any sort of speed. Could give the same to all ancients, make it an observation ship. But we would have to give the ancient facilities an ability to scan and see whatever level cloak it is so it would be harder for the Vorlons and Shadows to spy on each other.