You don't give a time frame of your trip, so I will try to cover multiple possibilities, but will assume it is in the near future.
When I took the Cap, it seemed like the right side of the train had better scenery out of DC. The Potomac River is on the right for more of the trip and the mountainside is fairly close on the left with a fair amount of tree cover so there wasn't as much to see on that side. I recall there is a large CSX (that or maybe NS, I don't remember exactly) yard on the left side of the train just before Cumberland if you like that sort of thing. I did it in winter so it was getting dark before we got to Cumberland. Looks like after Cumberland, the rivers are more on the left side of the train. Not sure how much of that will be in light with the mountains around.
DC:
Assuming you are coming in on the Crescent to WAS, you may want to be on the left side of the train, if you can, as you will be able to see the city as you cross the river and the Washington Masonic Temple in Alexandria right across from the station. As I recall, most of the rest is just trees and suburbs (including my neighborhood on the left in Springfield) until Alexandria and then you travel in an area behind buildings but not close enough to the river to really see anything there until the Potomac crossing. After that, the train is mostly in a covered trench and tunnel, so not a whole lot of note to see unless you like urban infrastructure.
Depending on your activity level desired, you may want to consider a 1 day capital bikeshare plan to get to the monuments around the mall. (www.capitalbikeshare.com). It is $7 for the day and each ride has a free half hour at the beginning. If you are not familiar with the concept, you pick up bikes at stations and drop them off at other stations, so you don't have to worry about locking up a rental or finding a place to store/park it. There is a station just outside union station and another near the Vietnam memorial (21st NW and Constitution NW). That area of the city is mostly flat and the distance between is only 2.6 miles (google estimates 17 minutes on a bike), so it would probably be comparable to or possibly faster than a taxi depending on the traffic in that area and you will be able to bike on the large paths along the mall and get in some extra sight seeing.
I've never eaten in Washington Union Station, so I can't speak to whether any of those are any good. I'm sure they are fine. I do like and suggest you consider the Mitsitam Cafe in the American Indian Museum (There is also anther capital bikeshare station nearby (Maryland and Independence Ave SW) The food is different from what you'll find a lot of places and I think the best among the museums (I have not eaten at the museums in a while though and I know they have been making efforts to provide better options). The place is buffet style with stations so you can pick what you want and it is reasonably quick depending on the time of day.
Another good option in my opinion is Hill Country bbq's pop up at the National Building Museum (5th st NW and F st NW). They run a more limited menu (
http://www.hillcountrywdc.com/assets/file/HCDC-Summer-Barbecue-Flyer-6.3.pdf) than the main location that isn't much further away (http://www.hillcountrywdc.com/menu), but I have found the crowds at the building museum to be lower than the main restaurant and it is fairly quick due to the limited menu as well. These are the only places I am familiar with that are quick and not crazy expensive near the area you want to be in. It has been several years since I tried to have lunch near the mall, but at the time it was rather difficult to find things that were not just hot dogs from a cart or McDonald's. From looking around, this cafe (http://westwingcafenjdc.com/lunch_sandwiches.html), this place (http://www.allmenus.com/dc/washington/277979-billy-goat-tavern--grill/menu/), and this restaurant (http://www.viewmenu.com/art-and-soul/menu) have pretty high ratings and are in the immediate area of the Station or along the route to the Memorial, but I have no experience with them.
CVS:
In Charlottesville, Maya (
http://www.maya-restaurant.com/) is right near the train station and was very good when I ate there a year or two ago. We didn't go to any of the others near the station. That said, L'Etoile (
http://www.letoilerestaurant.com/) and Continental Divide (
http://www.urbanspoon.com/cities/108-charlottesville/restaurants/853101-continental-divide/menu) are also right next to the station and get good reviews.
The rotunda is just under a mile away from the station and right down the main street of town, so if the weather is nice and you are up for it, it is a pleasant walk. No big hills, just the one the school is on at the end. If there is a big game at UVA or it is graduation time you will probably want to plan on walking there as the traffic will be rather crazy.
I didn't try to store bags in CVS, but as there is baggage service at the station, they may hold bags for you.
I second the recommendation to forget about Monticello. While I think it is worth a trip, it is rather inconvenient to do it quickly and without a car. It is just far enough out of town to be a hassle and the place is big enough for you to not really get a sense in just an hour or two. Also depending on the time of year, the road there can get jammed with people going to Carter Mountain Orchard. I've been in traffic in late summer/early fall that lasted for at least an hour to get by the mountain entrance which is before Monticello. If you plan a longer trip, Ash-Lawn Highland is also right there and is being restored so you can see the process and the before and after if you are into history.
Hope you enjoy your trip
All the layovers are scheduled to be several hours. We know that if the train arrives late, all our layover plans may go out the window, but I'd like to plan for the best.
