My dd and I have taken the AT a few times staying on both levels in coach as well as the sleepette. Here's my take...in coach we were on the upper level and yes there is a bit of swaying. On the way down (Fri) it was really crowded and no room to spread out so sleep was not comfortable at all. The bathrooms on were on the lower level and while there was a smell, it was nothing compared to the regular amtrak (Boston-Miami). We've done that one also and I vowed "never again". Back to the AT, one the way back from Sanford (Tues), our car was virtually empty which made relaxing and sleeping a much better experience.
Last December, we took the AT using the sleepette, I stayed on the bottom "bunk" and could definitely feel the wheels of the train bumping along on the track. I eventually went to sleep but I would not call it restful. On the way back, we were placed upstairs and while I did not feel the "wheel/rail" bumpiness, I definitely felt the sway and jarring of the train. Each time I drifted off, the train would jar and wake me up again. That said, my DD(15) slept like a log on both legs of the trip. The bathrooms on the sleeper side were not odor free (I believe that is just the nature of the train) but they were usable.
The food on both trips was decent. I am thinking about using the AT again for a 2012 trip, probably will do coach unless I can get a fab deal on a sleeper. Hope this helps.