Microsoft CEO Steve Ballmer (L) shakes hands with Skype CEO Tony Bates during a news conference on May 10, 2011. (Justin Sullivan/GETTY IMAGES)

The Windows maker does not have the best reputation for successful acquisitions. In the wake of the news, tech pundits and analysts have commented on the company’s past “botched” purchases and “less than enviable” track record of integrating new businesses. That could hurt Skype even more than other acquisition targets, notes tech blogger Om Malik, since the Skype team is “full of hired guns who are likely to move on to the next opportunity rather than dealing with the famed Microsoft bureaucracy.” Without the founders in place—Niklas Zennstrom and Janus Friis now run their own venture fund—there may be less loyalty than usual geared at keeping Skype true to what made it worth buying in the first place.

That said, there are reasons Microsoft’s bet could pay off. Microsoft CEO Steve Ballmer is keeping Skype CEO Tony Bates in place, having him report directly to the CEO. That should help to limit some of the aforementioned bureaucracy and give Ballmer, reportedly a direct champion for the deal, ready access to Skype’s performance and resource needs. Bates, a former Cisco executive, is hardly a died-in-the-wool entrepreneur who will chafe at the tech giant’s corporate culture, which could help get the initial integration off to a better start.

In addition, this is Skype’s second large corporate owner in just two years (eBay bought Skype in 2005 and then sold it 2009 after the acquisition faltered) and one has to hope the people who worked there at the time learned something from the process. At the very least, even venture capitalists who’d like to see Skype’s founders back in charge think the company is better off in Microsoft’s hands—the Redmond giant needs Skype to compete with Apple and Google, after all—than in the hands of eBay, which treated the Internet calling service more like an experiment than a competitive strategy.

Still, the forces working against the deal’s success are big ones. Purchases of small innovative businesses by big companies routinely stumble as two opposing corporate cultures try to work together. Supposed synergies don’t pan out once the product features or service offerings are linked. Add to that a business in which the road to profitability is already rocky—Skype posted revenue of $860 million last year and $264 million in operating earnings, according to the Wall Street Journal, but still had a loss of $7 million—and the pressure of successfully integrating the business while trying to record profits make the transaction exponentially more complex.

That’s why business leaders who try to navigate this notoriously tricky process should treat acquisitions more like partnerships than purchases, some experts suggest. In a 2009 Harvard Business Review article, professors at Rice University and the University of Pennsylvania’s Wharton School showed that keeping a distance between acquirers and their targets can bring together the best benefits of a merger without mucking things up with its inevitable complexities.

Whether or not it’s in Microsoft’s DNA to keep the Skype acquisition at arm’s length and not bog it down with bureaucracy remains to be seen. Even if Microsoft had the best buying record in the world, the deck would be stacked against them: Some 70 percent of acquisitions by corporations fail, according to some estimates. Ballmer and his team should probably take to heart Skype’s slogan (“Take a deep breath”) and loosen the reins on their new business a little. Sometimes the best way to manage something this complex is by simply letting go.

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