I have not followed teh case enopugh but to put in my 2C.

1.) As an Os and tool Vendor Msoft whould provide all the API's available to a 3rd Party developer - they are buying the tools.

2.) API's for things like office are a bit grayer - though msoft purports to expose some of them. These could be reasonable be kept separate - if they are not wound into the base OS.

3.) .NET is an interesting question in general.

4.) The difficulty of removing IE from the OS is more of an issue.