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Microsoft still doesn’t have much to show for its $8.5 billion Skype acquisition — except for a lackluster Windows Phone app — but Tony Bates, the former Skype CEO and now president of Microsoft’s Skype division, has at least managed to keep his ship independent of the software giant.

“We’ve kept our identity and our autonomy,” Bates told the New York Times in an interview.

How so? He’s based out of Silicon Valley (Skype also has offices all over the world); he demanded Skype-specific ID cards for his employees, instead of Microsoft cards; and perhaps most daring, he uses a MacBook Air in his office.

Skype now has nearly 250 million users, a 26 percent jump over the past seven months, the NYT reports.

Bates’ demand for freedom is understandable — Microsoft has been known to kill innovation as it absorbs interesting products into its Borg-like corporate culture. But it’s also dangerous, since Skype’s true value to Microsoft is the promise of deep integration across all of its many services. Skype is still working on bringing its service to the Xbox 360 (though that likely won’t happen this year), and Microsoft’s business-oriented Lync product, among other Microsoft services.

It may be tough to see now, but once Microsoft and Skype figure out a way to work together, the video chat service could end up being an even more powerful and ubiquitous force in our homes. Integration in the Xbox 360 will bring Skype to the living room, and it’s already available on most smartphones and tablets. But I wouldn’t be surprised if Microsoft pushes Skype as a standalone service as well, perhaps with more Skype handsets (which could potentially be powered by Windows Phone).

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