1) Linux and other unixes were created with the idea of privilege separation and permission baked in. Windows had to add it later, while keeping compatibility

2) Linux has a variety of kernels and libraries versions across its base, making it difficult to exploit it uniformly

3) MS is indeed capable of making secure OSes, I don't deny it, but you should not use Xbox, Windows Phone and RT as examples, since all three of them can ONLY install approved software (less for RT, but it's not used by end users in the same way)

4) MS could have used the same approach used by Linux and Android (and partially OSX): have a central approved and monitored repository of software, but giving the possibility to add external software by jumping a few hoops, i.e. inserting a password, or checking a couple of checkboxes before allowing untrusted installations.

5) To prove the point, Android has malware almost exclusively outside of the google play store. Never heard of someone getting malware by using android, while I know an handful of people getting malware on windows (this is anecdotal experience, but I don't have any other data)

6) The shitstorm was raised because on some Secure Boot implementations it was impossible to disable it