Rule 1: Hire an expensive, internationally renowned architect to create a jarring, distinct, and ostentatious design to please architectural critics and hopefully win a prize.
Rule 2: for the love of God make sure you have a large grand hall that you can rent out to wedding groups and for diplomatic occasions. Remember just because you’re subsidized by 35 million people doesn't mean you can afford to get cheap.
Rule 3: have a grand entrance to allow the people bask in the glory of the design. Don't worry about putting anything really at all in the grand entrance, the aforementioned superiority of the architectural design will pummel the visitors submission.
Rule 4: This is really important, don't forget to include the actual exhibits in your museum. The public will spend exorbitant amounts of money to get into your museum, even though you’re a public institutions, so they will expect to learn a thing or two. Make sure to keep it as impressionistic as possible. Remember taxpayers aren't paying for specific facts.
Rule five: Be sure to refer to your national museum as world class at every available opportunity. If you don't, people might realize, I mean, er, suspect that your full shit.
Review: When looking at the floor plan of the museum, if exhibits are a clump in the middle of everything else, instead of everything else a clump middle of the exhibits, you know you've done a good job. They only complain because they're jealous.