Did you wait in the regular line with the stroller or did they ask you to use the wheelchair line? I thought I read somewhere that strollers should use the wheelchair line.
Most of the lines are "Mainstreamed", which means that the regular line is accessible.
When you get the Guest Assistance Card/tag that allows you to use a stroller as a wheelchair, ask for a park map for guests with disabilities for each park.
They list the entrances for people using wheelchairs/
ECVs/strollers as wheelchairs.
In most cases, the Guidemap does say to use the regular queue.
We were there just a month ago and DS (6) uses a large medical stroller. The rides that we had to use a special line for were - PP, IASWAA, Hall of Presidents (had to take an elevator up), Kilimanjaro Safaris and Jungle Cruise to name a few.
Most shows also had a separate line as we were seated in the back row with wheelchair seating. Only Monsters, Inc, COP and Tiki Birds were the only ones I can remember where the seats were not in the last row. This was really good for us though in that if the seats weren't filled DS could talk and it would not disrupt everyone around us.
Believe me some waits in the wheelchair line - most notably KS were extra long as they would bring in a whole truck for the accessible line.
I think you have mixed up American Adventure with Hall of Presidents. At the AA in Epcot, the entry to the building is on the ground floor, but the entrance to the theater is up a flight of stairs (also have some escalators). For guests with wheelchairs/ECVs/special needs, there is an elevator to get to the 2nd floor. Hall of Presidents is all on one floor.
Some of them, like Small World and Kilamanjaro Safari, you enter thru the regular line and follow that until you get to a wheelchair pull-out point because the regular boarding area is not accessible.
At Jungle Cruise, they may have you wait in the regular line or there is a handicapped area line - because of the number of people who are waiting there, the wait is sometimes longer than the regular line.
regarding shows - last year when we saw Nemo, w/c was in the very front and it is NOT a good place! DS could hardly see the stage.
There are actually 3 wheelchair viewing areas at Nemo.
One is in the very front and I agree with you that it is difficult to see from since the stage is actually above you. There is also a small wheelchair viewing area in the middle of the theater. The majority of the wheelchair seats are in the rear.
As has already been stated many times they will route you to the regular standby line with a stroller as a wheelchair in many rides. What I do in cases like this is bring a blanket and place it over the stroller (if fastpass is unavailable). DD can feel as though she is "safe" and doesn't have to look at everyone around her (eventhough THEY usually look at HER-I wish I had a sign that said staring is rude sometimes!). Earplugs can work for the noise. For us, we know the rides so well now that we hit the rides that have the wheelchair accessible standy lines early when there is a shorter line and less crowds (not to mention she hasn't yet hit overstimulated point) and avoid those in afternoons or near mealtimes. However, the wheelchair alternate entrace rides can be longer waits but you're away from the crowd so the wait doesn't seem longer because you're not enduring your child reacting from the crowd. As was also stated the handicap seating in the various shows can either be in the front or the back. This is very important to note for sensory sensitive kids. We sat in the front in Lion King and it was just too much (lights, fog, movement)-wish I had thought ahead and realized we needed to be in the back as that show is difficult to quietly get up and leave if needed when you're in the front.
Just a heads up - because Lion King has stadium seating, the only seating you don't need to climb stairs for is in the front few rows. The other seating is above floor level and you can't get out except on the floor.
I've never done the handicap accessible seating for a parade as it's not needed however, they can become dicey when others squeeze in and bump dd's stroller.
We have used the handicapped accessible areas for a few parades and suggest checking it out ahead of time. The spots for some of the day parades are directly in the sun with no shade.
Those areas can also get very crowded and they tend to park the wheelchairs/strollers/ECVs practically touching each other across the front of the viewing area. Even if you have no one next to you to start with, as more guests come, they may end up parked right next to you and your family's spot will be behind the stroller/wheelchair.
If you find your own spots outside of the handicapped viewing areas, you will have the ability to keep a member of your party on each side of the stroller, which may work better for you.
The handicap accessible entrances are confusing in so many rides, so we just do the best we can and mainly use GAC for common areas and places that don't allow normal strollers at all such as all the very large buildings where a meltdown would make it very difficult to exit or in lines with a very long queue.
The new Guidemaps are more helpful than the old booklets. The maps look very much like the 'regular' park maps, but have additional information, like where the handicapped entrance is for each attraction right by that attraction on the map.
I have been advised that my son is definitely not autistic.) Having said that, I'm sure that some of the tips for autistic children may help him. 
