The ATC is not as smart as real ATC controllers, so it has an unfortunate tendency to suggest you fly into mountains. Use your best judgement and avoid doing so. ;) You may have to cancel the ATC flight and file again from mid air so that ATC picks you up again.
The taxi route depends on how the taxi lines were drawn by the scenery artist, if applicable. If it has auto-generated ATC routes, it is unsurprising if they are unrealistic. I looked at KBNA in WED, and it appears it does not have hand-drawn taxi routes, so the autogenerated ones are going to be illogical.