A lot of this is personal bias, but I actually prefer DC in the fall. Spring gets second vote. But what I love most about the fall is side trips. For example, you can easily get in your car and do Skyline Drive (Shanendaoh Mts) in less than a day, and it's breathtaking.
I also think VA is the place to stay. Crystal City and Rosslyn/North Arlington are excellent if you plan to spend all your time in the city. But you're also well positioned if you want to hit nearby fun stuff, like Old Town in Alexandria. This is a fun venture. It's just a series of little shops and restaurants, and you're basically heading east/south until you hit the Potomac. Then you turn around and do the other side! It's funky and fun.
Back in the District, definitely Air and Space. Make sure you save time for the IMAX films, whatever they're showing. And I, too, loved the Holocaust Museum, but it's not for everyone. It's depressing, but fascinating at the same time. Another place that can get overlooked is the National Cathedral. I'd lived there about 10 years before I saw it when my stepmom came to town. This isn't the type of thing I normally seek out, but I loved this tour.
One other idea. Make the Capitol/Congressional buildings one of your first stops, and visit your Congressperson and Senator. They always have a lot of good, current tourist info. Also, if you're interested in touring the White House, as soon as you know the dates of your trip, write or call both Senator and Congressperson. These tours are only available if you have tickets and you get them this way.
The one other item I can add is that DC and close in metro is a lot smaller than most visitors are anticipating. The Pentagon in Northern VA, for example, is about 5-10 minutes by car from the White House. Well, except for rush hour.