But what stops factions sending the damn thing into every battle if it's so potent in pvp? People love to win. Give them a tool that really ups their chances at coming out of a brawl on top and they -will- spam it. ths reducing the 'omg, here's comes the boss' feeling you may have when it appears seldom.
Im all for this, but Im worried about how people will wave their uber stick.
Read carefully. Maintaining these ships would be -expensive-.
Perhaps introduce a possibility that equipment from the flagship will fall off if it gets destroyed. Considering all flagship stuff is expensive and might be produced via player bases...yeah, it's a tough deterrent.