As noted earlier, seats in the new BART trains are uncomfortably high. SF Muni made the same mistake with their new light-rail trains, but at least they have now corrected the problem:
Design changes will come to the next batch of trains based on passenger feedback Muni has received since the arrival of the new trains. The transit agency plans to lower the seats by two inches, including on trains that have already arrived, and also provide different lengths of hand straps and an archway handhold in the middle of the train.
BART really needs to fix this as well.
Systemic Failure 
If I recall, they were made higher to better accommodate the elderly and others who have trouble walking. If so, this might be the first instance of rolling back an ADA change.