In its blog post announcing the acquisition of 6Wunderkinder (the company behind Wunderlist), Microsoft is at pains to emphasise there won't be any changes in the short term:
Customers can expect the app to remain free in all of its existing markets. There will be no price changes for Wunderlist Pro or Wunderlist for Business customers and the service will continue to support a wide range of third-party apps and integrated services.
Long-term, greater integration with other products is expected, and Office 365 is the obvious candidate. The closest parallel is probably with Microsoft's acquisition of Skype -- a product which has maintained its own brand and is available on a range of platforms, but is particularly tightly integrated with Windows.
Welcome 6Wunderkinder! Microsoft acquires Wunderlist [Official Microsoft Blog]