We - me, my sister and my mum (in a wheelchair) - rode the ride twice while there in September, and had problems both times. The first time put off us completely, and it was only thanks to a special fastpass that we went on a second time.
The first time we went in the regular queue, which was a 40-minute wait. We got around with everyone else fine, until we got split to go up the wheelchair loading bay, where by we joined a queue of 4 or 5 other parties. That was okay, but we then stood and watched as the people who were behind us in the original queue, get up the stairs, over the bridge, on the ride and out before we even moved anywhere. It was another 40-minutes before we got on that ride from the wheelchair loading bay.
The wheelchair car was taking forever to come around - I think they only had one in operation. Not sure if there is just one car, or that a second was not working, but it took a long time to get everyone loaded and around. That put us off going on again because if we were going to have to wait twice as long as the stated time (which after that ride never got below 65mins), then it wasn't worth wasting part of our day.
Like you said Sue, we also found that it was a long time between pulling the car off the main track and putting it back on the track. Several cars were going by before our car was put back 'into action'. It is certainly something they could improve on. Once we were on, it was fine, and getting off too.
The second time we used a fastpass, so went straight around to the loading bay. It was still a good 15mins before we were loaded, but at least this time around they checked if we were able to transfer, and when we said yes, they pulled a standard car into the loading bay. However, we didn't end up back there, at which I was totally livid.
As we realized we were going to the normal loading bay, my sister and I were waving frantically at the guys on the controls going 'wait, we're supposed to be over there!' But we ended up in the main loading bay and were expected to unload quickly. My sister and I had to leap out of our side of the car and run over to the wheelchair, which had been left at the furthest possible point away from our car, and bring it back over.
We left mum in her car until we brought the chair over because she can't move easily (swollen ankles and knees make getting up and moving very difficult) and generally needs a hand. By this time though, those in the regular queues we virtually jumping on her to get into the car, and the CM was very rude insisting that she could take just a couple of steps to get out so they could load.
That's what we liked about the whole Toy Story set up - that as a disabled guest your loading/unloading was separate from the normal running of the ride and you could take as much time as you needed getting in and out without disrupting everyone else. Only the time we weren't sent to that loading bay, it caused all kinds of problems.
For anyone offered a standard car because they can transfer, might be wise to insist that they are returned to the disabled loading bay in order to disembark at their own pace.