Minify scripts served by the ScriptManager
Bundling is a cool idea, but it doesn't always play nicely with the ScriptManager when used in a webforms scenario. I would like to propose the ability to set a flag on the ScriptManager that would allow it to minify the combined scripts its serving.
We actually added some support for the bundling system to the ScriptManager in .NET 4.5. It doesn't do the bundling itself, but rather can understand the contents of bundled scripts to ensure any duplicates are removed. The 4.5 project templates in Visual Studio 2012 use this functionality.
A change to actually allow the ScriptManager to create a bundle from the scripts you reference is a much more complex change, due to the existing composite script support and long legacy of integration with the rest of System.Web (Update Panels, Ajax controls, etc.).