I think there is at least something to the story...I think some of the inconsistencies can easily be attributed to the lack of attention that would be given to someone who would do something like this anyways...why should they know that it's called Fastpass and not Speedpass (which exists but is something else) if they don't even use it?
I have been to Disney many times with my brother who is in a wheelchair. There are very few lines that you actually "cut" and it is usually just and alternative entrance that is accessible. There are more times than not that we have waited for it's a small world, thunder mountain and splash mountain longer than the actual line. Now this is not busy season, but it is not what most people think. Most rides now have accessible lines and we go through the regular line. Plus we are pulled to the side to wait for the wheelchair car or to wait for them to slow down the belt or ride car.
Things are a bit different for someone who uses and wheelchair or
ECV merely for transportation, and does not need it on the rides themselves.
In December 2010, my father in law was with us. He has Parkinson's Disease, which in his case manifests itself with difficulty walking. He could certainly walk short distances, say to get on/off an attraction, although he might need extra time on some of the moving attractions like Buzz and HM.
He didn't do any of the coasters or anything like that, but here are some things of note, as we did not experience as much "mainstreaming" as expected.
Haunted Mansion - on approach, we were directed to the exit. We had to wait a short time as a KTTK tour was coming out, but we were then loaded in from the unloading platform. Got to see the corridor in between, but didn't get to do the stretching room or anything.
IASW - on approach, we were directed to the exit queue. We waited a short time as there were a few people on
ECVs ahead of us, and they loaded one group from our line per boat. No one needed to wait for the WC-accessible boat. The main line wasn't terribly long, but we still boarded before most of them.
Buzz Lightyear - We were told to use the Fastpass line. Dealing with the turns with the ECV seemed easier in that line. We waited for a few to be loaded from the standby line, and then boarded.
Toy Story Mania - We had Fastpasses, but on approach we were directed to the Fastpass line with the ECV and never asked for the passes. After getting to the join point, we were then diverted directly to the accessible platform. Here is where it was interesting - we waited a LONG time. There were several families ahead of us, two with a wheelchair that could not transfer. There is a special WC-accessible car that holds only two people, coupled with a normal 4-person car. It appears there is only one of them, so we had to wait for that car to come around, get unloaded, loaded again (which with the WC takes time as there is a ramp, and they have to secure the WC, etc.). And then wait again for it to come around, unload, load, etc. They didn't divert a standard car pair to the platform, even when the WC-accessible car wasn't needed.
I can pretty much guarantee that in that case, we waited longer than the standby line.
Those are the ones that I remember being the exception to the mainstreaming. 3 out of 4 appeared to be an advantage.
Since he didn't do any of the more thrill-level rides, I don't know how those may have been affected, but from my own experience it doesn't seem that as much as been mainstreamed as expected.