I think the main problem with flak is not so much that it is too powerful (though that is likely the case as well), but that it is so much better at PD than other PD weapons, even ones that cost more OP. The heavy burst laser for instance is 13 OP but is worse at destroying missiles than even regular flak which is 8 OP.
As for the ship system idea, I assume you mean a system that converts an amount of soft flux into half that amount of hard flux? That actually sounds pretty interesting. I think it might work better that it simply converts all of your soft flux into half (or some other fraction) that of hard flux, since whatever amount of soft flux is lost is always countered by the amount of hard flux gained. Using the system would allow you to keep firing weapons at the present at the cost of forcing you to lower shields sooner in the future, a short term gain for a long term disadvantage. It would be most interesting on a ship with low armor, good shield efficiency, moderate speed, decent flux dissipation, and a relatively large amount energy weapons. The focus of shields over armor means that monitoring your hard flux levels is more important as tanking hits on the armor while waiting for the hard flux to be vented is a more dicey proposition. If the ship is too fast than it will always be able to retreat to vent, thus mitigating the downsides of using it, but if it is too slow than it will not be able to retreat and using it may be too risky. Similarly, it shouldn't have so little flux venting that you would always take more flux damage simply by waiting for it to go down, but not so much that waiting is always the better option. It should use energy weapons as those tend to generate more flux to fire, making the system of more importance than if it used ballistics.