That aurora loadout is fine as a flagship, I've used very similar loadouts before (although I tend to prefer omega weapon based loadouts since they were added). With EMR (and possibly missile spec from skills), two sabot pods will last for the whole fight (they are only needed for cruiser/capitals anyway). The reapers are enough to nuke 2-3 capital ships or 5-8 cruisers, and the player knows how to save them for the right moment. Smaller ships will just die to 2x HB. With skills and hardened subsystems, the CR is enough for everything but the most extreme multi-capital brawls.