If you are staying on property, the easiest way to get to Trail's End is by boat from the Magic Kingdom which is wheelchair accessible. It takes you from the main dock right opposite the security checkpoint in the very centre of the tapstyle gate line. The journey takes about 15 minutes and is very pleasant.
At the other end it is about 3 or 4 minute flat walk to the restaurant. The only slight issue with disabled accessibility that I can think of is that the restrooms are located outside the restaurant itself which would require you to go out and around the corner, there is a small ramp. This is worth remembering if you have kids or anyone who may need help during the meal.
The location of Trail's End is probably why it is not popular as people can't be bothered to go on the boat. We try and do it on a MK day and come out for a break before the Electrical Parade and Fireworks.
The restaurant is not open for lunch only breakfast and dinner. There is a great selection of food and it is super friendly. I have been with a wheelchair user, someone who has a large electric wheelchair and he had no difficulty getting up to the buffet. There is not usually a frantic line like you get at Boma or Crystal Palace at times.