The goal when designing a longer-distance train schedule usually works like this:
- First, try to design a daytime schedule where most people going between major origins and major destinations are on the train less than, say, 8 hours. What, it just takes too much time between cities to do that? OK, then...
- Try to design a "get on in the evening, get off in the morning" schedule for the major "too far apart" cities, and design a daytime schedule for other more popular cities.
- In short, you get worse ridership when you serve a station at 2 AM, so you're trying to avoid that at major stations.
But the thing is, when you're trying to serve a very long string of cities, and you have to accomodate the needs of the host railroads, the need for refuelling and servicing, the need to connect with other trains, etc. etc. etc., you can't really do this. So all schedules end up being compromises.
An example: the Coast Starlight carefully plants the overnight segment of the trip between the southernmost popular station in Oregon, and the northernmost popular station in California. The rest of the schedule is determined by that, and by how fast the train can go on the tracks, basically. This ensures that all popular stations are reached during the daytime, which tends to help ridership.
Another example: the Lake Shore Limited can provide "on in the evening, off in the... midday" or "on in the... midday, off in the morning" service between NY and Chicago due to the trip length. The "on in the evening" and "off in the morning" is located at Chicago to maximize connections, and because there isn't much ridership from the vast empty spaces across Indiana. Whereas NYC gets the "midday" times, because it still allows for "on in the evening" (or "off in the morning") in upstate NY, which generates a lot more riders. The eastbound schedule is further distorted by trying to meet late connections from west of Chicago. This schedule causes later-than-desired arrivals across the whole of NY and Amtrak has been talking about moving it back to the more "natural" schedule.
If you look at most of the train services with these thoughts in mind, you start to see the logic behind them. A few of the really odd schedules are driven by trying to get equipment to its maintenance base, which can even determine routings (if Amtrak had a maintenance base at Tampa rather than Miami, you can bet the Florida trains would be arranged differently).