My guess is that Microsoft will rewrite the multiplayer server modules first, replacing Java with C#. They will introduce standardized APIs (that the game sorely needs). Expect to see micropayment systems introduced. Then I would expect a move to Azure cloud services, replacing the dozens of multiplayer server farms that are out there. Games will finally support more simultaneous characters per world, larger worlds, etc. and actually scale.
By this point you will see a schism in the developer community, those that hang on to the old server code and those that begin migrating to the new cloud-based (supported) code. XBox will enable access to Azure-code servers (today you can only access a world hosted by another XBox player), and that mode of play will quickly become dominant. Mods will be developed in Visual Studio 15, with a new project type.
As Microsoft continues to extend .Net to Apple and Linux environments, they will release new clients for those environments in .Net only. Expect some tie-ins with Microsoft Phones to check in on your Azure-hosted worlds, etc like Microsoft SmartGlass does for Xbox.
The Minecraft Client will be updated slowly, in a way that most people won't realize that Microsoft is tweaking it. When they finally release a v 2.0 client, I imagine that all existing accounts will be converted to Live accounts, whether you like it or not. One day out of the blue, it will block access to Java-based servers citing a "security risk to your Live account". You can keep playing with your old client on old servers, but you wont get the new widgets, textures, etc. The server hosting community will continue to dry up, until you convert to the new client through inertia.