I think you are over estimating how much energy is recovered during braking. Each full energy square that comes up on the 15 minute consumption screen represents 30 Wh. Under long controlled braking, where you make sure only reg braking is used by not allowing the power meter to go off the scale and therefore not engaging the mechanical brakes, you may get three full square if you are lucky, which is 90 Wh.
The IS300h battery capacity is just under 1500 Wh, so you have charged the battery 6%. Even if we accept that really little more than 50% of the true battery capacity is available for use (the in-build redundancy makes the Toyota system ultra reliable) you have still only achieved around 10% recharge - the rest is coming from the petrol engine, through sustained re-charging, whether the battery indicator shows this or not.
The next gen Toyota hybrid system, used in the current Prius and which will be used in the new Lexus UX, is a big step on. The batteries are able to be recharged at a higher rate, allowing for better regen, the inverter and transmission are more efficient, and electric only modes can operate at much higher road speeds. Even with this system you see a drop in mpg at motorway speeds compared to free flowing urban driving.