Well the main thing to consider is that it's not possible to restrict a passenger's movement around the bus. A wheelchair user would be treated just the same as a normal passenger, i.e. they'd go upstairs on a double decker and sit inside existing seats. While you theoretically could make a wheelchair user, the game isn't designed with them in mind so it wouldn't work too well.
The best solution I could propose would be a little similar to the Chicago bikes - nobody is carrying a bike when they are at the stop, nor do they walk off with one when they leave, but a bike is on the front of the bus while they are. Equally nobody would board or disembark in a wheelchair, but one would magically appear beneath them when they sit in the wheelchair bay seat.