I think everything should be taken into account, aerodynamics and all.
As stated earlier, just because you get better efficiency in one aspect doesn't mean the overall efficiency will increase or distance per fuel unit spent per person/unit-of-mass will increase either.
- If your vehicle were a solid lead mass, then the amount of energy that could be lost to braking would be much greater than the amount of energy lost to aerodynamic drag. Say the difference is about 90% of inertial energy would be lost during braking and the other 10% to air drag and rolling resistance. If regen is 90% efficient then the total amount of inertial energy that could be recuperated during braking is 81%.
- If your vehicle has the total mass of a feather, then the amount of energy that could be lost to braking is hardly anything and nearly all of it will be lost to aerodynamic drag. If the difference is 50% of your inertial energy is lost to aerodynamic drag and rolling resistance, then it doesn't matter if regen is 100% efficient. You will never recuperate more than the remaining 50%.
- Mind you both vehicles will need to eventually accelerate. The one withe the mass of solid lead will need a whole lot more energy to accelerate. The one mass of a feather will need a whole lot less.
- As aerodynamics and rolling resistance are improved the more all the inertial energy will need a braking effect in order to change it. If a car has 0 aerodynamic drag and 0 rolling resistance, all the inertial energy will have to be either lost or recuperated by some form of braking.
- Something else to take into account is electric motor and controller efficiency curves. A high performance system may be less efficient at low regen currents than higher ones. As a result, it becomes more efficient when there's more mass to slow down. But the same result could be achieved by lowering mass and the performance of the motor and controller. Acceleration would be essencially the same since the power to weight ration would be essencially the same.