In the midst of a series of changes to its service and company, Skype may have a new chief as well. The New York Times cites Tony Bates, an executive from Cisco Systems, as the possible new hire at the VoIP firm.

Bates will reportedly be joining the Skype team by the end of October, and a blog entry from Cisco confirms Bates departure to pursue other things.  Cisco’s existing CTO, Padmasree Warrior, will take on the role of SVP/GM for the company’s Enterprise, Commercial and Small Business Development Group.

From the Times,

Tony Bates, who leads the networking giant’s enterprise, commercial and small-business unit — a division with $20 billion in annual revenues and about 12,500 employees — will assume the top job at Skype as its new owners continue to put their stamp on the fast-growing company after buying it from eBay one year ago.

It seems it wouldn’t be a bad move for Skype, as Bates has led a number of communications initiatives at Cisco. Skype in particular is seeking more ways to integrate its product into devices, networks and other tools–something it’s slowed down on in the past year or so.

Since separating from eBay, which acquired the VoIP service in 2005 for $2.6 billion and later admitted overpaying, Skype has leveraged its brand and the talent behind it to weather economic hardships and an inflated product line.

More recently, Skype has taken several steps to improve its positioning for the telecom revolution, including going after an IPO and partnering with Facebook for deep integration with the social network. A change in the executive line up indicates Skype’s determination to further shift its direction and footing for the future.

In other news, Cisco has been developing a number of telecom products for businesses and home office use.