This way, you can place breakpoints in the .js file and they would magically fire. You then have full use of Visual Studio's powerful debugging tools, such as the Immediate window, Watches, and the ability to mouse over a variable and see its value. This is really key; if Microsoft wants us to write more client side code, then we had better have all the weapons in our arsenal to be able to debug it!
"Edit and Continue" also still kind of works. If you change code in a .js file (or even markup in an .aspx or .ascx), just save the file, and refresh the page in your browser. Visual Studio's debugger stays attached, and you can very quickly tweak your UI in this manner.
Then, I noticed the following during one of the first times I debugging code in Visual Studio 2008:
This is awesome, because although I totally embrace new technology doing menial tasks for me, I hate when too much is going on behind the scenes...especially to the point of me not understanding how something works. Visual Studio 2008 is un-abstracting all the magic that ASP.NET does to convert our managed code to web pages.