I could be wrong, I might be missing something significant here but, do flagships have any special properties that make them worth keeping around? Furthermore, what is the point of being able to designate a starbase as a flagship ala Starbase Mobilization? For that matter, how do you even perform that task as I've never seen an option to do so? It would be great if flagships actually conveyed some sort of bonus in combat or morale. Also, if Starbase Mobilization actually meant you could zip around the galaxy destroying entire armadas or at the very least, produce ships from your starbase.
So am I missing something, or are these just unfinished ideas that never became implemented?