We really aren't sure yet whether we'll use the site to book our travel. We wanted to have the choice of booking with the site, without being forced to book with them. The site seems to have decent deals for where we want to go (Hawaii), and they have great customer support to come up with unique packages. In the past we've been "do-it-ourselfers" when it comes to planning our vacations, but Hawaii has so much to it that we will probably need some help.
When we picked a site, our first priority was to verify the security. Finding a site without fees but with verified secure transactions proved to be elusive. So we figured that if there was going to have to be fees, we wanted everyone to feel comfortable with the site. We also wanted everyone to be able to call in case they weren't comfortable with web transactions.
Beyond security and resonable fees, we looked for a site that we could personalize to reflect our tastes, etc. You can upload your own photos, write your own descriptions for the different components...and even add password protection to your registry so that only your guests can view it (we wanted as much privacy as possible).
Anyways, now I'm rambling...but I hope the info helps you make your decision.