I believe it has to start at PvP, and work down to PvE. The AI is so stupid it has to use buffed systems and weapons, and when those items are taken to PvP the balance goes out the window.
Another thing- weapon mounts need to be an assigned type (i.e. energy, torpedo, etc) and kept non-interchanagable. NO race would build a torpedo only ship, or a beam only ship so why should the players be allowed. This 1:1 weapon interchanagability thows balancing ability off. Anyone ever see a torpedo only AI ship ? Not me.