In my simplistic analysis, I think Microsofts biggest problem is trying to be everything to everybody. Also, jumping on the bandwagon way late (zune).
Aside from that though, when you're worth close to 300 billion its kind of tough to get past that no matter what you do. Too many forces against you at that point.
Can somebody say Dept. of Justice? Now apple is feeling the heat from the feds with music.
