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First of all, let me say that I have absolutely no inside knowledge of what Microsoft is doing and why. That said, I have followed Microsoft for over 15 years and understand how they think.
Microsoft's InterestMicrosoft's primary interest is in controlling virtualization of Windows operating system instances. They want to be able to prevent customers from running Windows in a VM outside of licensing restrictions through WGA. In a conventional VM, that is impossible. In order for Windows running in a VM to be able to ensure it is within the license restrictions, and be controlled by WGA, it must be able to peek into the real hardware in a way that cannot be hacked. Microsoft is developing a way to control this through software.
Microsoft charging for use of its IP is legitimate from Microsoft's point of view. This is understandably offensive from VMWare's point of view, the pioneer in the field, and a "partner" contributor to the Microsoft ecosystem.
Server hardware is going to get much bigger and much faster as we move forward. Running Windows server instances in virtual machines in
production is going to be more and more important and more prevalent. Linux can run in virtual machines very well and competes with Windows Server. So, it is important for Windows Servers to be able to do it well also. And, it is important for Microsoft to be able to enforce licensing restrictions. They could do it by having close face-to-face relationships with customers (e.g. the way IBM's mainframe business is run). But, Microsoft's approach is to control their customers around the world remotely from Redmond automatically through WGA.
What's wrong with this picture?This is just another excellent example of Microsoft exercising its rights to improve Windows and compete (with Linux in this case) while systematically destroying a "partner" that is in the way. In this case, it is VMWare, the pioneer in the field of PC virtualization.
Without antitrust help, VMWare is toast, just like so many other dead "partners" that have suffered the same fate for the same reason. In the future, Windows will not be able to be successfully activated on any other VM technology except Microsoft's, or licensed "partners" carefully controlled and manipulated by Microsoft. Bank on it.
ISV "partners" in the Microsoft ecosystem often suffer a premature death.
How SHOULD this play out?There should and could be a balanced solution to this. Microsoft's needs for Windows Server competition should be met. Also, VMWare's contribution to the Microsoft ecosystem should be respected. My version of a balanced solution looks something like this:
- Microsoft should not have been permitted to buy Virtual PC nor give it away for free.
- Microsoft should define requirements for Windows running in a VM.
- Virtual PC and VMWare should be permitted to use the spec without charge.
- Should Virtual PC and VMWare fail to build great VM solutions that enable Windows Server to compete very well with Linux, Microsoft should develop its own VM technology that competes with Virtual PC and VMWare. But, that technology should not be given away for free. It should COMPETE in the marketplace. If Virtual PC and VMWare are really inferior, the Microsoft solution will win on merit.
How WILL it play out?This is only my prediction. But, I think I'm right.

Microsoft simply does not work like I describe with "partners". ISV "partners" in the Microsoft ecosystem are merely pawns to be sacrificed whenever the time comes, and come it always does.
Microsoft will take care of its own interest to the exclusion of VMWare's. VMWare is toast, sooner or later. EMC might sue Microsoft over antitrust. If it does, the Microsoft fanboys will cry "whiner whiner whiner" about EMC and VMWare just like they always do when Microsoft systematically destroys a former ISV "partner" through abuse of its monopoly power.
Also toast: Running Windows in a VM on Macintosh.
The End (for VMWare and Parallels)
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Postscript: What SHOULD be done about it?I am no fan of government regulation or socialist governments. I favor capitalism. But, sometimes there needs to be some limitations when there is a powerful monopoly like Microsoft rolling over everybody else with its absolute monopoly power.
The U.S. federal government should step in and force Microsoft to protect its interests without destroying the ISV "partners" in a way like I described.