From watchingbones.com:

Bones without Booth? What kind of show would that be? Well, that’s the show we almost got, if it hadn’t been for the chemistry between Emily Deschanel and David Boreanaz. Turns out that originally, the show was slated to have Brennan as a single lead with Booth’s character as just a limited supporting role. Booth was planned to be in 13 of the 24 episodes in the first season, while Brennan was going to interact with other cops in addition to Booth.

While it took a little while to cast the leading man, David Boreanaz was suggested to Hart Hanson and he jumped at the chance to sign him. He said, “I thought he could be funny. I underestimated him. He can be very funny.” Brennan’s character turned out to be an even bigger challenge. Emily Deschanel was recommended by a friend of Barry Josephson’s who had worked with her on the movie Glory Road. She fit the role, but unfortunately she wasn’t quite as easy a sell for all those involved.

Apparently, Boreanaz wasn’t thrilled with Deschanel at the very beginning, and “challenged” her to step up to the role. According to Hart Hanson, “David had another actress he liked, that he thought should be the lead. David’s a very strong-willed man. So he… I wouldn’t say sabotage… he challenged Emily to rise to the occasion by advancing on her.

David’s about 6′1?, and about 200 lbs of shoulders with pecs attached, and the ‘package’ and knees… very, very… he’s a guy… And he advanced on her in the network test. And Emily stepped into it. She stepped right toward him. And then they had one of the exchanges that we used in the pilot. And it was when even a thick-head like me went ‘whoa.’”