I think the priority targeting system is fine most of the time, but it'd be nice to have a little more control which ships your fleet targets first. Maybe take out their transports so if you lose the battle you won't lose your planet. Or if they have a capital ship with crazy defense and little escorts with no defense, take out as many little guys as you can first before you tackle the "priority" target.

Of course this means you might want to also implement fleet formations so you can make sure your transports are protected and don't get targeted first.