Where I think Microsoft innovates is in offering software suites which work well together. I don't think they innovate very much on each individual product so I agree with you there, although there obviously have been certain innovations in the .NET family of products and in DirextX. There's a reason the Mono software project was started. That article you linked to seems written by somebody with an agenda, and he's probalby wrong on a lot of points, not that a lot of points aren't valid as well. That's the problem with many people in general -- it's either black or white and no grey, and I really don't think like that.
A company can get a Windows network up and running with Exchange, lots of tools for development, etc., and everything just works nicely together. With Linux, a more inexperienced I.T. admin is either going to have a complete failure or very difficult time getting things up and running. Where Microsoft wins is ease of use in terms of setup. Now, I can get a Linux server up and running with just a terminal and no GUI but that's me and I am a small percentage of people who have that kind of knowledge and experience.
You can also say Microsoft innovated in the sense of their business strategy which made them successful. Innovation isn't necessarily a term only applying to the technical side of things. In this link I've linked to before, you can see one of the Microsoft developers commenting that he thinks NT is better in some ways over Linux. Maybe he's right?
Look: Microsoft still has some old-fashioned hardcore talented developers who can code circles around brogrammers down in the valley. These people have a keen appreciation of the complexities of operating system development and an eye for good, clean design. The NT kernel is still much better than Linux in some ways --- you guys be trippin' with your overcommit-by-default MM nonsense --- but our good people keep retiring or moving to other large technology companies, and there are few new people achieving the level of technical virtuosity needed to replace the people who leave.
http://blog.zorinaq.com/?e=74 Microsoft has a checkered history and engages in bad business policies as far as their embrace, extend, extinguish practice, and I also believe they voluntarily handed over whatever data NSA wanted about anyone through the PRISM program. I also think they tip NSA off about security holes in Windows before they're patched, and there also may be a possibility that Windows has built-in backdoors. What's funny to me is the level of information people need to be flooded with until they believe something to be true. For instance, Mark Klein, William Binney, and Thomas Drake apparently weren't enough to convince the masses of any spying program until Snowden came along. And even now, people are more interested in playing Pot Farm. Microsoft's innovative business strategy, at least as far as Windows is concerned looks to be facing a major uphill battle. Even though there are a ton of desktops out there, a lot of people are complacent with older versions of Windows. By the time security patches run out for Windows 7, Linux may start to be seen more often on the desktop, and more people will be switching over to tablets.