The Charger of the DJI Phantom 3 Professional offers is offering 100W (17,5V 5.7A) and it needs about 60 minutes to charge the intelligent battery. Its smaller 57W version, provided with the Phantom 3 Advance, needs up to 100 minutes. Note: The thermal protection of the intelligent battery prevents charging if its too hot (directly after the flight) or if its too cold.This improves battery life.
Both charger versions are able to charge the internal 2S, 6000mAh of the remote controller as well.
Its tempting to charge them at the same time, but don´t do this: Its never a good idea to charge batteries with different sizes (capacity/voltage) parallel or supply different charger electronics by the same source. Charging the empty flight battery, the charger starts with app. 15.6V, continues with 16V (second LED) and ends at 17.5V (all LED blinking). Time vs. Voltage behavior while charging the smaller Flight controller battery with its own charging electronics is different. You won´t save time anyways.
Same goes for parallel charging of multiple intelligent batteries. Although several auction sellers will earn money with fancy adapters, allowing to connect several batteries at one charger, its not recommended, since they never have the same charge state or internal resistance. If multiple charging is required, its better to use separate chargers or chargers with truly separated outputs, which should not exceed the 17,5V max., mentioned before,and should not be below, since balancers usually need a voltage higher then cell voltage for proper operation.