I think the OP wanted to include only urban or suburban stations to exclude rural Amshacks that only serve a handful of passengers on a once-per-day (or less frequent) train. If we want to generate some sense of priorities for station improvements, reconstruction or replacement, those stations, provided they are safe and functional, would be lowest on the list.
Heavily used stations (or stations that could be if service was better), should be higher priority. I've never seen it in daylight, but I think Cleveland would qualify, as would Cincinnati and Indianapolis (though I've never been to the latter two.) These stations (and much of the Midwest) would very likely be very high traffic stations if Amtrak medium and long distance service was improved (e.g. multiple daily trains to Chicago), and there was local commuter rail or light rail service. (I don't think any of these cities has any public transit except buses.) Local public transit should ALWAYS be integrated with Amtrak.
More traffic would justify rebuilding or replacing bad stations, and if you need to rebuild or replace, it is not much more expensive to build a nice station, or rehabilitate a decrepit but formerly beautiful station. I bet they could even make a TV show about it "This Old Terminal"
BTW, Atlanta's station isn't ugly, but it is small and inconvenient to public transit. (It's quite a long walk to the subway, about a mile, there were signs on the road in front for a bus route, but I never saw a single bus, and the closest bus stop was a couple of blocks away.) It's plain-looking, no auxiliary services such as food or a convenience store, has a very small parking lot, and the elevator is apparently broken. If there was day-time service to Washington and/or N Carolina on the existing route, and especially if there was Tennessee/Chicago and/or Florida service added, rebuilding or massively expanding the station would be well justified. (Maybe at a different location.)
