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While the method of displaying advertising on Skype does seem a bit "in your face", almost literally, I think it is reasonable for a company to want to monetize its products. Without a profit motive, why would companies devlop anything (assuming that a given company is a traditional, for profit entity)?
You can use the paid version of Skype and get it ad free. Or do what I do with most of my friends: use Google. Skype isn't the only game in town.