One change that probably most of you are going to like is that the compilation model is more like ASP.Net 1.x, where the .aspx file will now by default remain separated from the code-behind binary when the code is pre-compiled. In beta 1, the pre-compilation compiled even the .aspx pages together with the code-behind.

The reserved application_xxxx folder will now use the "app_" prefix. For example:

Beta 1              October CTP                Beta 2

\Code               \Application_Code         \app_code

There will be a new CTP version probably released in November with those changes.

Read more about the ASP.NET 2.0 product design changes between Beta 1 and Beta 2