Sounds good, and maybe it can be spiced up a bit if we give some special weapons to then but those can be built only on player base modules. And make those modules to require the maximum leveled base and expesive materials.
Give a power core buff to these flagships and raise the power consumption of the flagship weapons. Maybe a single flagship turret can require as much enegy as a BS Cerb, or even more so other normal battleship can't use them effectively.