I can't imagine more than a half day for the Spy Museum and even that much would only be because it tends to be so crowded. Near to that is the Museum of Crime and Punishment (which I have not been to). There's also the Newseum if you're into pricey visits (but the exterior is interesting and free).

The FDR Memorial is new since you've been here and, even after the cherry blossoms are gone, the walk around the tidal basin (which includes that and the Jefferson Memorial) is a pleasant one.

The Natural History Museum has a hall of mammals which has been entirely redone. The Museum of the American Indian is relatively new and the cafe there is alleged to be the best on the mall. I like the Botanic Gardens and the Library of Congress as well. The Building Museum has its moments and has a particularly good gift shop.

I think you'd be able to find enough to keep you busy for three days. If things within the district pall, you can always go wander around Old Town Alexandria. And there is a lot to be said for just meandering around the city.