Is Microsoft more innovative, or is Microsoft simply more publicly innovative? Apple (and tons of other companies, for that matter) simply don't make hay out of their R&D efforts until they have something sellable to announce.
If one is to assume R&D spending it roughly equatable with "non-public" innovation than historically Microsoft is more innovative than even Google, let alone Apple. This assumption may be weak but I think it would at least be somewhat correlated.
