I propose to go forward with creating new governor restriction specific to various ship types for acceleration which is not dependent on thrust and weight.
High end cargo ships should be limited by what the governor allows. Something like 4.5G's plus the amount allowed by purchased inertial mitigation technologies. Low end fighters would then be limited by thrust, while high end fighter would be limited by the governor limit of around 8.5G's plus inertial mitigation technology allowances.
I think adding governor and inertial mitigation will make it possible to set perfect balance to the ships in the future after adding specific limitations depending on realistic variables.