I find it interesting that Disney seems to have issues with mobility devices on their buses that other mass transit systems don't have. Disney buses are in no way special compared to any other bus based mass transit system, and there is plenty of experience out there dealing with mobility devices.
Where I live, there is an extensive bus and bus rapid transit network. Wheelchair loading is common, maybe not to the same extent as Disney, but when it happens it not nearly as big a deal. "Regular" mass transit systems have an even bigger issue with trying to reduce dwell time than Disney does, since they are scheduled while Disney buses are not. At home, a bus will pull up to a stop, be ready to load a mobility device in seconds, and be ready to depart in less than a minute or so. There are a few factors that help with this:
The ramp is at the front door.
Most major mass transit systems I've seen seem to prefer this, though there are exceptions. A front ramp means the driver can remain in their seat while the ramp flips out. The rear doors can be smaller, possibly allowing for more seating. The bus only has to kneel to the front, and not to the side as well, simplifying mechanical. An issue with low-floor buses is the space between the front wheels makes it difficult to turn the mobility device, however all three major North American bus manufacturers (Nova, New Flyer and Gillig) produce buses that allow an ADA compliant device to maneuver easily, and all three brands of bus are already operating at Disney World. Disney has certainly tried front ramps before, as almost any manufacturer demo will be equipped with a front ramp, and photos of the articulated demo buses from New Flyer and Nova not too long ago confirm they had front ramps. A front ramp also means the passenger gets to board through the same door as everyone else, so there is no special or different treatment. This can also make it easier to load mobility devices from the same lineup and as everyone else, since as people board they just keep moving back into the bus, not blocking the path of the wheelchair.
Mobility devices face backwards and and not necessarily secured.
This is a major time saver as the driver does not have to get out of their seat to secure the device. This is both a policy and equipment issue. In order to allow devices to ride unsecured, the system has to passively hold the device in place. At home this is accomplished by having wheelchair riders ride facing backwards, and back their device up against a padded backrest behind the wheel well. There are belts available, but I have never seen them in use. Some systems that use this system still require the device to be secured however, for liability or other reasons. In this case, it may be worthwhile for a system like Disney that has a large number of wheelchairs to invest in something like the "Clamp Device" that was mentioned. This type of device does exist, and means the mobility device can be self secured without the help of the driver. You can see it here:
http://www.qstraint.com/en_na/products/transit-solutions/quantum
In summary, all of the issues people seem to have with wheelchairs are based on Disney's own decisions. There may be reasons for these decisions we don't know about, but if wheelchair loading is a major issue, then there are ways of making it better without adding an extra fleet of buses.