If you replaced the Naboo hanger with the Federation Landing craft hanger (where Qui-Gon and Obi-Wan drop out of the vent) Maul could be waiting for them there as the last obstacle.
They could land on the ship in the guise of ambassadors (but at the end of the film instead of the beginning) and the space battle could take place while they fight to get first to the bridge and latter to the secondary control in the reactor station.