The title says it all. We are visiting Rome in a few weeks. If we only have time for one, which? And why?
The Capitoline Museum for sure, for the site and building itself, the treasures it contains, the breadth and depth of its collection. While I love the National Museum of Rome, it is definitely a second-tier museum. The focus is more on the city during the last few hundred years, which is fascinating but not as comprehensive as the 2500-year sweep of history represented by the Capitoline. If you have time, see both, but otherwise pick the Capitoline. Both museums are rarely crowded.
Capitalone would be my choice.