This is similar to the change Vanguard made in 2005, when they stopped using indices licensed by Dow Jones and adopted ones licensed by MSCI.
an article written at the time of that change. The change was made without any problems as far as I know.
The present change is being made for the same stated reason--Vanguard wants to pay lower licensing fees. It sounds like they locked in a very long-term deal with the Univ of Chicago for use of the new benchmarks. In addition, if the new indices will reduce the amount of trading required by fund managers (as Vanguard claims they'll do), that will reduce costs.
Still---with all the recently unearthed deals (manipulation of LIBOR, etc), I'm probably not the only one who wonders if there's not the potential for "influence" in the selection of stocks to join/be dropped from various benchmarks. As indexing has gained popularity, having your company's stock included in a popular index creates instant demand for it, increasing the stock price. That might be worth a donation to an individual or institution to assure "fair" treatment.