Food does get pricey fast, especially if you eat in or near the Smithsonian. If you do that, its probably worth it to get a membership to the Smithsonian for the discount. And, as someone said, after walking, walking walking, most people don't go three blocks out of their way and back to get to a Subway or McDonalds.
Likewise, you'll pay for either transportation or convenience - either way you'll walk a LOT. Staying near the Mall will mean you can walk most places - but you'll spend more per night on your hotel room. Staying out will mean you take the Metro in and have those fees. If you are counting dollars, do your math - and do keep in mind that the Metro Passes that are cheaper aren't going to get you anywhere during rush hour - so you'll be arriving a little later to the museums (which is probably fine, it isn't Disney World).
Watch the museum hours. When we were there, there was at least one popular museum that had extended hours into the evenings each day.
If you want to see the Holocaust Museum or Ford's Theatre, get tickets in advance (both through their website). Get tickets to the Bureau of Engraving through your Representative. There is a small charge for advanced tickets for the first two - but its a very small processing fee.