As far as the protected wetlands aspect, with the new plans for the buildings the Imagineers are actually "adding to the wetlands" because each building's footprint will occupy less square footage than the original buildings, hence "adding" more square footage to the wetlands.
With ADA, I believe accessibility for handicapped individuals (i.e. stairs only w/ no ramps to second floor) were at issue as well.
I believe the new buildings will not have living quarters in the lower level, the top floor has been re-situated to accomodate all the living quarters.