<p>If you create an ASP.NET web file project you have direct access to the Profile information in the web.config file. If you convert that to a Web App and have been using ProfileCommon etc. then you have to jump through a whole bunch of hoops to get your web app to work.</p>

<p>Why wasn't the Profile provider built into the ASP.NET web app projects like it was with the web file projects?</p>

The profile provider uses the ASP.NET Build Provider system, which doesn't work with Web Application Projects.
Adding a customized BuildProvider
  class to the Web.config file works in
  an ASP.NET Web site but does not work
  in an ASP.NET Web application project.
  In a Web application project, the code
  that is generated by the BuildProvider
  class cannot be included in the
  application.
source:
MSDN Build Provider documentation