To me this seems like a bit of a double-standard. Do Microsoft want you to run Windows Update to patch the problems in their operating system? Or do they want you to run this "malicious software removal tool" to remove the malicious software, but not patch it?
I imagine Microsoft will also struggle to ever include adware removal as part of this package. As soon as they release a tool to automatically remove software voluntarily installed by the user, however annoying, they'll become a big target for lawsuits.