With the exception of EMH and park closing getting from park to park in a wheelchair is really easy and not crowed at all. Using the monorail is very easy and quick and using the buses you are the first one on and last one off but there is almost always a spot for you.
As long as you avoid the most crowded times of park openings and closings you will be fine on WDW transportation. You may have to wait a little longer as the service is spread out more during the non-rush times, but you will be fine.